CN102063580A - System and method for virtual reality simulation of monomolecular dynamics in nano-environment - Google Patents
System and method for virtual reality simulation of monomolecular dynamics in nano-environment Download PDFInfo
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Abstract
The invention provides a system and method for virtual reality simulation of monomolecular dynamics in a nano-environment. The system comprises a monomolecular optical detection system, a molecular physical environment parameter control system, a data conversion interface and a virtual reality system. The data of monomolecular spatial position, spatial orientation and luminous intensity obtained by the monomolecular optical detection system is called by the virtual reality system through the data conversion interface to realize the simulation and display of the monomolecular motion and luminous characteristics in the nano-environment; and the molecular physical environment parameter control system is connected with the virtual reality system through the data conversion interface, thus realizing control on monomolecular motion states and luminous characteristics. According to the invention, the functions of three-dimensional dynamic display, dynamic simulation, real-time interface and the like are available, and a research platform and technical support are provided for the research and control on the monomolecular dynamic characteristics in the nano-environment.
Description
Technical field
The present invention relates to the unimolecule optical detection and control technology, computer virtual reality emulation technology, be specifically related to nanometer environment the place an order virtual reality emulation system and the method for molecular dynamics.
Background technology
Virtual reality is the environment that computing machine generates, and by the environment of simulation and simulation of natural reality, the user can incorporate wherein, places oneself in the midst of in the real event seemingly.It provides fine approach for the displaying directly perceived of a lot of abstract things for people understand this things better.Along with the development of high-resolution laser spectrum Detection Techniques in recent years, Optics detection of single molecules becomes technical possibility under the nanoscale.Because measure a large amount of period of the day from 11 p.m. to 1 a.m that divide, the ensemble average signal that obtains can be covered the characteristic of each molecule, and the single-molecule detection technology can be eliminated this ensemble average experimentally.Monomolecular dynamics comprises translation, rotation and the characteristics of luminescence etc. of molecule.The single-molecule detection technology can be implemented under the nanoscale the dynamics of certain specific molecular and this molecule and the observation of physics environmental interaction on every side, simultaneously optical monitoring and follow the tracks of monomolecular technology biological, chemistry with physically all have a very wide range of applications, as the measurement for monomolecular dipole orientation can be applied to that observing protein is folding, the macro molecules of proteinase, complex and actin etc. moves.Owing to individual molecule can be made good response to the current/voltage variation of physical environment around it, unimolecule can be applied to the sensor of nanoscale category simultaneously, but this has very important significance for the monomolecular probe technique tool of development; Monomolecular in addition detection and manipulation technology also have great importance to preparation unimolecule light quantum device.
Adopt virtual reality technology and to control monomolecular motion process and luminescence feature is showed visually, be convenient to understand intuitively the unimolecule dynamic characteristic optical detection; Change monomolecular physical environment parameter simultaneously in virtual program software, the unimolecule dynamic process is controlled in simulation.This has significant values for research and application unimolecule.
Summary of the invention
The object of the present invention is to provide a kind of nanometer environment the place an order virtual reality emulation system and the method for molecular dynamics.
The place an order virtual reality emulation system of molecular dynamics of nanometer environment provided by the invention comprises unimolecule optical detection system, molecular physics environmental parameter control system, data transformation interface and virtual reality system; Described virtual reality system comprises computing machine and virtual reality applications software, is used for the analog demenstration to molecule and background environment model, and to the Simulation Control of molecular motion and luminance; Described data transformation interface comprises data converter, data collecting card and digital input-output card; By data line, data collecting card is connected with the unimolecule optical detection system, and digital input-output card is connected with molecule environmental parameter control system; Data collecting card obtains the Molecular Graphs picture of unimolecule optical detection system collection and the data of luminescence feature, gives virtual reality applications software by the data converter assignment; Simultaneously the data of unimolecule physical environment parameter in the virtual reality applications software are changed by data converter, output to molecular physics environmental parameter control system by digital input-output card, be used for controlling respectively electric current, voltage and the temperature of unimolecule physical environment.
Utilize virtual reality to develop software and design the human-computer interaction interface of virtual reality system application software, this software adopts the windows window interface of standard, comprises menu, quick botton, emulation show area, molecular parameter show area; Menu comprises that data file, Molecular Selection, motion control, external force controls four modules, finishes the read-write of unimolecule dynamics data file, monomolecular selection, the analog simulation operation of unimolecule motion and calling of molecular physics environmental parameter control module; Under the menu of software interface, place function button to finish part funcall commonly used; The emulation show area is used to represent the three-dimensional graph of unimolecule and background environment, and the operator can use mouse that specific molecular is selected, and follows the tracks of specific monomolecular motion; But the specific monomolecular position coordinates that molecular parameter show area Dynamic Display operator selectes, spatial orientation and luminous intensity information and molecular physics environmental parameter information;
The unimolecule optical detection system comprises two parts: single molecular fluorescence imaging device and single molecular fluorescence sniffer.The single molecular fluorescence imaging device can obtain the data of monomolecular motion trace data, unimolecule luminous intensity and the information of monomolecular spatial orientation according to difference image constantly simultaneously to a plurality of unimolecule imagings in the confocal plane; The single molecular fluorescence sniffer is used for the definite individual molecule luminous intensity of directly monitoring and the variation of degree of polarization.
Molecular physics environmental parameter control system comprises voltage, electric current and temperature control equipment, can realize voltage, electric current and temperature environment parameter control.
The place an order virtual reality simulation method of molecular dynamics of nanometer environment provided by the invention comprises the steps:
A. set up the virtual reality scenario model of unimolecule, background molecule, electrode and conducting film:
A1. make up monomolecular three-dimensional stereo model;
A2. set up the three-dimensional stereo model of liquid background and solid-state background molecule;
A3. make up the electrode in the unimolecule physical environment of living in and the three-dimensional stereo model of conducting film, according to electrode physical size in the experiment, proportionally be provided with three groups of electrodes to be measured around monomolecular, conducting film is designed to the Two dimensional Distribution of spherical molecule;
A4. the three-dimensional stereo model of conversion structure is the data layout that Virtual Reality Modeling Language can call, and preserves;
B. set up the description of monomolecular locus and spatial orientation:
Monomolecular locus by (z) three-dimensional rectangular coordinate is determined for x, y, and its spatial orientation is by α and two angle-datas decisions of θ:
Monomolecular locus coordinate can be determined according to following formula:
Wherein (x y) is the brightness of molecule hot spot in the unimolecule image, c to f
0And c
1Be scale-up factor, x
1And y
1It is fitting constant; By setting the luminance threshold of unimolecule hot spot, near the certain limit the speck center, the molecule hot spot is carried out match with following formula, can obtain x, the y coordinate information of molecule.The information of coordinate z can obtain by the symmetry feature of analyzing molecules hot spot.
Monomolecular spatial orientation α value can be expressed as:
Be fluorescence light intensity on two orthogonal polarization directions that P (t) and S (t) send for unimolecule wherein, the θ angle obtains by the space asymmetry of analysis list molecular imaging hot spot.
C. the unimolecule luminous intensity is described:
C1. the pixel brightness value of changing unimolecule hot spot in the image that the single molecular fluorescence imaging device passes back is a unimolecule relative luminous intensity value, by the virtual reality applications software transfer, and the monomolecular luminescence feature of emulation;
C2. the signal data of changing the acquisition of single molecular fluorescence sniffer is a unimolecule relative luminous intensity value, by the virtual reality applications software transfer, and the monomolecular luminescence feature of emulation;
C3. the unimolecule relative luminous intensity value that step c1, c2 is obtained is carried out normalized;
D. set up the motion model of unimolecule in liquid background, and the dynamic characteristic model under the different physical environment parameter:
D1. set up the motion model of unimolecule in liquid background; Its model can be expressed from the next:
λ wherein
xBe the root-mean-square displacement of molecule random motion, t is the time, and R is the liquid constant, and T is the absolute temperature of the physical environment of molecule, and N is an avogadros constant, and k is a coefficient of viscosity, and P is a molecular radius.
Unimolecule dynamic characteristic model when d2. setting up the external electric field change in voltage; Unimolecule is as an electric dipole, and under the effect of external electric field E, suffered moment can be expressed as:
Wherein q is an electric charge, and l is the direction of electric dipole moment of molecule.Can find out that thus the electric field force that the molecule of different spaces orientation is subjected in external electric field as electric dipole is different, its size depends on the angle of spatial orientation and electric field E.It is different that different rotating torques cause the convergent speed of the orientation of different molecular.
D3. set up the physical model that the luminescence feature of molecule under the function of current changes.The luminescence feature model of molecule under the function of current can be expressed as:
Wherein η is a scale-up factor, has different scale-up factors for different unimolecules, it by experiment data fitting obtain; N is luminous photon number,
Energy for photon.According to law of conservation of energy, when electric current I process molecule, current changing rate equals the variation of molecular fluorescence.
The fluorescence of molecule produces owing to electronics transits to ground state spontaneous radiation process from excited state.Under the function of current, electronics in the molecule and outer field current generation electron exchange.The probability size that the excited state electronics is transferred in the size decision molecule of electric current, thus molecule spontaneous radiation change of luminous intensity caused.
E. realize being connected of virtual reality system and unimolecule optical detection system and molecular physics environmental parameter control system:
E1. data collecting card is gathered the data that the unimolecule optical detection system is surveyed, enter data converter, locus and spatial orientation according to molecule among the step b are described, obtain monomolecular relative position coordinates, spatial orientation data, these data save as position coordinates, the spatial orientation data file is called by virtual reality system;
E2. data collecting card is gathered the data that the unimolecule optical detection system is surveyed, enter data converter, luminous intensity according to individual molecule among the step c is described, and obtains monomolecular relative luminous intensity data, and these data save as the luminous intensity data file and called by virtual reality system;
E3. the molecular physics ambient parameter data of virtual reality system output is stored as the ambient parameter data file, after being read and changed by data converter, outputs to digital input-output card, connects molecular physics environmental parameter control system by data line; Be used for controlling respectively electric current, voltage and the temperature of unimolecule sample physical environment.
F. realize the place an order virtual reality emulation of molecular dynamics of nanometer environment by virtual reality applications software:
F1. the human-computer interaction interface of virtual reality applications software adopts the windows window interface of standard, comprises menu, quick botton, emulation show area, molecular parameter show area; Menu comprises that data file, Molecular Selection, motion control, external force controls four modules, finishes the read-write of unimolecule dynamics data file, monomolecular selection, the analog simulation operation of unimolecule motion and calling of molecular physics environmental parameter control module;
F2. the model of unimolecule, background molecule, electrode and the conducting film by call establishment realizes that in the emulation show area three-dimensional display of unimolecule and background thereof and various visual angles observe;
F3. virtual reality applications software is realized the emulation of unimolecule translation, rotary state and luminance by calling the data file of molecule position coordinates, spatial orientation, luminous intensity to the state parameter assignment of unimolecule three-dimensional stereo model;
F4. the control module of environmental parameters such as design voltage, electric current and temperature in the virtual reality applications program according to the description of step e, with the numerical value that the environmental parameter control module is returned, realizes controlling the actual environment parameter by data-interface.
Compared with prior art, the present invention has realized the virtual reality emulation of molecular motion state and luminescence feature under the nanometer environment, the unimolecule dynamic characteristic of nanoscale can be showed visually.In virtual reality scenario, realized by changing molecular physics environmental parameter controlling to the molecular dynamics process.By being connected of virtual reality system and real experimental provision, realize the co-operating that virtual reality and true environment are controlled.Not only can onlinely controlling and show, also can off line demonstrate operation, is unimolecule optical detection and the good combination of controlling technology and Computer Control Technology under virtual reality technology, the nanometer environment.Given prominence to the applications well of dirigibility, pre-operation and the illustrative of virtual reality technology in research nano molecular dynamic process, for the experiment porch that provides good is followed the tracks of and controlled to the unimolecule in the nanometer environment.
Description of drawings
The place an order virtual reality emulation system synoptic diagram of molecular dynamics of Fig. 1 nanometer environment
The 3-d modelling figure of Fig. 2 Cy5 luminescent dye molecule
The 3-D solid structure model of Fig. 3 glycerol molecule
The macromolecular three-dimensional model of Fig. 4 organic long-chain
Fig. 5 unimolecule three-dimensional rectangular coordinate and the explanation of spatial orientation angle
The Cy5 luminescent dye molecule image that Fig. 6 single molecular fluorescence imaging device obtains
The movement locus of Fig. 7 unimolecule in the xy plane
The software interface of Fig. 8 virtual reality emulation
Fig. 9 voltage control module three-dimension virtual reality scene
Figure 10 current control module three-dimension virtual reality scene
Embodiment
The place an order virtual reality emulation system (as Fig. 1) of molecular dynamics of nanometer environment of the present invention comprises: virtual reality system (man-machine interactive system) 1, data transformation interface 2, molecular physics environmental parameter control system 3, unimolecule optical detection system 4, unimolecule sample 5;
Virtual reality system (man-machine interactive system) 1 comprises computing machine and virtual reality applications software, by calling the data of data transformation interface, analog simulation unimolecule dynamic characteristic, and realize the emulation of unimolecule dynamic characteristic is controlled by changing unimolecule physical environment parameter;
Data transformation interface 2 comprises data converter and digital input-output card, data collecting card, realize between virtual reality system 1 and molecular physics environmental parameter control system 3 and the unimolecule optical detection system 4 data-switching be connected; Data collecting card is gathered the unimolecule image of unimolecule optical detection system acquisition and the experimental data of luminescence feature, calculate the data that obtain monomolecular position coordinates, spatial orientation angle, luminous intensity by data converter, assignment calls for virtual reality applications software again; The data of molecular physics environmental parameter control module output in the virtual reality applications software are changed by data converter in addition, output to molecular physics environmental parameter control system by digital input-output card;
Molecular physics environmental control system 3 comprises: voltage, electric current and temperature control equipment, and molecular physics environment control module 4 is connected by data line with digital input-output card;
Unimolecule optical detection system 4 comprises: single molecular fluorescence imaging device and single molecular fluorescence sniffer; Unimolecule optical detection system 4 is by data line and data acquisition card connection; The unimolecule optical detection system is realized with method described in " being used for monomolecular method of fast optical tracking and device thereof (publication number CN101655460) " and device thereof.
The place an order embodiment of virtual reality simulation method of molecular dynamics of nanometer environment of the present invention is that example specifically describes in detail with the Cy5 molecule:
A. set up the virtual reality scenario model of unimolecule and background molecule, comprising:
A1. according to the chemical constitution of Cy5 molecule, utilize the three-dimensional stereo model of chemical simulation configuration software Culgi structure Cy5 molecule, Figure 2 shows that the three-dimensional stereo model of Cy5 luminescent dye molecule;
A2. utilize chemical simulation configuration software Culgi to make up liquid background (glycerol molecule, as Fig. 3) and solid-state background (the big molecule of PMMA organic long-chain, as Fig. 4) the molecule three-dimensional stereo model, re-use based on the three-dimensional animation of PC system and play up and make the simplification three-dimensional stereo model that software 3dmax designs above-mentioned molecular model;
A3. use based on the three-dimensional animation of PC system and play up and make the electrode in the software 3dmax design molecule physical environment of living in and the model of conducting film; According to electrode physical size in the experiment, be provided with three groups of electrodes to be measured around monomolecular in proportion, be used to control the voltage under the nanometer environment; The conducting film design of Simulation is the Two dimensional Distribution of spherical molecule, and conducting film is used for the current delivery under the nanometer environment;
A4. change the model of above-mentioned structure, and save as the virtual reality scenario file, make virtual reality applications software seamlessly to call;
B. the description of unimolecule relative tertiary location and spatial orientation:
B1. μ is as a unimolecule (as Fig. 5), it at three-dimensional relative position by (z) three-dimensional rectangular coordinate is determined for x, y, and its spatial orientation is by α and two angle-datas decisions of θ.
Monomolecular locus coordinate can calculate according to following formula:
Wherein (x y) is (x, the y) brightness of the sub-hot spot of punishment, the c of coordinate in the unimolecule image to f
0And c
1Be scale-up factor, x
1And y
1It is fitting constant; The a plurality of monomolecular image that Fig. 6 returns for the single molecular fluorescence imaging device, a-e represent to have the unimolecule hot spot of different symmetry features respectively; Unimolecule imaging facula Luminance Distribution is obeyed the definition of following formula, set the luminance threshold of unimolecule hot spot, difference according to the speck size, in the fit range of setting, the unimolecule hot spot is carried out match, can obtain monomolecular x, y coordinate information, unimolecule the movement locus xy plane in of Fig. 7 for obtaining by the following formula match; The information of coordinate z can obtain by the symmetry feature of analyzing molecules hot spot.
Monomolecular spatial orientation α value can be expressed as:
Be fluorescence light intensity on two orthogonal polarization directions that P (t) and S (t) send for unimolecule wherein, P (t) and S (t) can be obtained by single-photon detector, and the θ angle obtains by the space asymmetry of analysis list molecular imaging hot spot;
B2. set up the relative position relation between unimolecule and the background molecule: unimolecule immerses in the liquid glycerin molecule; On the big molecule long-chain of unimolecule attached to solid-state background surface, along with big molecule long-chain rotates together;
C. the description of unimolecule luminous intensity:
C1. read the pixel brightness value of unimolecule hot spot in the image that the single molecular fluorescence imaging device passes back, be converted into unimolecule relative luminous intensity value, be used for calling of virtual reality applications software, the monomolecular luminescence feature of emulation;
C2. read the signal that the single molecular fluorescence sniffer obtains, data are converted to unimolecule relative luminous intensity value, be used for calling of virtual reality software;
C3. according to same monomolecular detection, the unimolecule relative luminous intensity value that step c1, c2 obtain is carried out normalized;
D. set up the motion model of unimolecule in liquid background molecule, and the dynamic characteristic model under the electric current, voltage effect:
D1. set up the motion model of unimolecule in liquid background molecule; Its model can be expressed from the next:
λ wherein
xBe the root-mean-square displacement of molecule random motion, t is the time, and R is the liquid constant, and T is the absolute temperature of the physical environment of molecule, and N is an avogadros constant, and k is a coefficient of viscosity, and P is a molecular radius.In the liquid background molecule under disturb in no outfield, the description of following formula is obeyed in the random motion of unimolecule and liquid background molecule.
D2. set up the unimolecule dynamic characteristic model under the voltage effect; Unimolecule is as an electric dipole, and under the effect of external electric field E, suffered moment can be expressed as:
Wherein q is an electric charge, and l is the direction of electric dipole moment of molecule.Can find out that thus the electric field force that the molecule of different spaces orientation is subjected in external electric field as electric dipole is different, its size depends on the angle of spatial orientation and electric field E.It is different that different rotating torques cause the convergent speed of the orientation of different molecular.
D3. set up the physical model that the luminescence feature of molecule under the function of current changes.The luminescence feature model of molecule under the function of current can be expressed as:
Wherein η is a scale-up factor, has different scale-up factors for different unimolecules, it by experiment data fitting obtain; N is the photon number of spontaneous transition,
Energy for the spontaneous transition photon.According to law of conservation of energy, when electric current I process molecule, current changing rate equals the variation of molecular fluorescence.
The fluorescence of molecule is to be produced from the spontaneous radiation process that excited state transits to ground state by electronics.Under the function of current, electronics in the molecule and electric current generation electron exchange, the probability that the excited state electronics is transferred in the size decision molecule of electric current, thus cause molecule spontaneous radiation change of luminous intensity.
E. realize being connected of virtual reality system and molecular physics environmental control system and unimolecule optical detection system:
E1. data collecting card is gathered the data that the unimolecule optical detection system is surveyed, enter data converter, relative position coordinates and spatial orientation according to molecule among the step b are described, obtain monomolecular relative position coordinates, spatial orientation data, these data save as position coordinates, the spatial orientation data file is called by virtual reality system;
E2. data collecting card is gathered the data that the unimolecule optical detection system is surveyed, enter data converter, according to the luminance model of individual molecule among the step c, obtain monomolecular relative luminous intensity data, these data save as the luminous intensity data file and are called by virtual reality system;
E3. the molecular physics ambient parameter data of virtual reality system output is stored as the ambient parameter data file, after being read and changed by data converter, outputs to digital input-output card, connects molecular physics environmental parameter control system by data line; Be used for controlling respectively electric current, voltage and the temperature of unimolecule sample physical environment.
F. utilize virtual reality to develop software and design virtual reality applications software, software interface as shown in Figure 8;
F1. utilize virtual reality to develop software and design the human-computer interaction interface of virtual reality applications software, this software adopts the windows window interface of standard, comprises menu, quick botton, emulation show area, molecular parameter show area; Menu comprises that data file, Molecular Selection, motion control, external force controls four modules, finishes the read-write of unimolecule dynamics data file, monomolecular selection, the analog simulation operation of unimolecule motion and calling of molecular physics environmental parameter control module; Under the menu of software interface, place function button to finish part funcall commonly used; The emulation show area is used to represent the three-dimensional graph of unimolecule and background environment, and the operator can use mouse that specific molecular is selected, and follows the tracks of specific monomolecular motion; But the specific monomolecular position coordinates that molecular parameter show area Dynamic Display operator selectes, spatial orientation and luminous intensity information and molecular physics environmental parameter information;
F2. the model of unimolecule, background molecule, electrode and the conducting film by call establishment, realize that in the emulation show area of the application software of virtual reality system the three-dimensional display of unimolecule and background thereof and various visual angles observe, use mouse or keyboard can adjust viewing angle; The Molecular Selection menu realizes calling different unimolecule models, background molecular model;
F3. the virtual reality system application software realizes the emulation of unimolecule translation, rotary state and luminance by calling the data file of molecule position coordinates, spatial orientation, luminous intensity to the state parameter assignment of unimolecule three-dimensional stereo model; According to the motion model of describing in the steps d 1, realize the motion simulation displaying of unimolecule in the liquid glycerin molecular background; The beginning of moving control module for controlling unimolecule motion simulation, suspend and stop, and can realize the unimolecule motion simulation put effect slowly;
F4. the external force operational module in virtual reality applications software comprises voltage, electric current and three modules of temperature:
The design voltage operational module, the adjusting of voltage swing realizes with slide block, and utilize the voltage switch of mouse control, the data of voltage to show in the molecular parameter show area, according to the model emulation unimolecule dynamic effect of describing in the steps d 2 that spatial orientation reaches unanimity under the voltage effect; Fig. 9 is a voltage control module three-dimension virtual reality scene simulation, and molecule is placed in the liquid glycerin background, and unimolecule presents the free movement state under the no-voltage effect; When the operator clicks voltage switch, interelectrode monomolecular spatial orientation changes, and all monomolecular orientations all reach unanimity; The data of voltage are output to data transformation interface simultaneously, are connected with voltage-operated device through digital input-output card, realize controlling real molecule;
Design unimolecule current control module, use the electric current of mobile electronic model emulation by conducting film, the adjusting of size of current realizes with slide block, and the current switch of design mouse control, realize current switch and size adjustment, the data of electric current show in the molecular parameter show area, dynamic effect according to model emulation unimolecule luminous intensity variations under the function of current of describing in the steps d 3, Figure 10 is a current control module three-dimension virtual reality scene simulation, unimolecule is placed on the conducting film, click current switch, electric current will flow through unimolecule, and its luminous intensity can change along with the size of electric current, the size of current difference that adds on three electrodes, unimolecule presents different luminous intensities, and electric current is big more, and the unimolecule luminous intensity is repressed obvious more; Current data outputs to data transformation interface simultaneously, is connected with current control device through digital input-output card;
The design temperature control module has designed radio button and has regulated temperature, and the data of temperature show in the molecular parameter show area, vary with temperature the variation of the motion state that is produced according to the descriptive model emulation unimolecule in the steps d 1; The data of simultaneous temperature output to data-interface, are connected with temperature control equipment through digital input-output card.
Claims (2)
1. the nanometer environment virtual reality emulation system of molecular dynamics that places an order is characterized in that comprising unimolecule optical detection system, molecular physics environmental parameter control system, data transformation interface and virtual reality system; Described virtual reality system comprises computing machine and virtual reality applications software; Described data transformation interface comprises data converter, data collecting card and digital input-output card; By data line, data collecting card is connected with the unimolecule optical detection system, and digital input-output card is connected with molecule environmental parameter control system; Data collecting card obtains the Molecular Graphs picture of unimolecule optical detection system collection and the data of luminescence feature, gives virtual reality applications software by the data converter assignment; The data of unimolecule physical environment parameter are changed by data converter in the virtual reality applications software, output to molecular physics environmental parameter control system by digital input-output card, be used for controlling respectively monomolecular physical environment parameter, comprise electric current, voltage and temperature;
Described virtual reality applications software adopts the windows window interface of standard, comprises menu, emulation show area, molecular parameter show area; Menu comprises that data file, Molecular Selection, motion control, external force controls four modules, finishes the read-write of unimolecule dynamics data file, monomolecular selection, the analog simulation operation of unimolecule motion and calling of molecular physics environmental parameter control module; The emulation show area is used to represent the three-dimensional graph of unimolecule and background environment, and the operator can select specific molecular, follows the tracks of specific monomolecular motion; But the specific monomolecular volume coordinate that molecular parameter show area Dynamic Display operator selectes, spatial orientation and luminous intensity information and molecular physics environmental parameter information;
Described unimolecule optical detection system comprises single molecular fluorescence imaging device and single molecular fluorescence sniffer;
Described molecular physics environmental parameter control system comprises voltage, electric current and temperature control equipment, can be respectively to the molecular physics environmental parameter, comprise that voltage, electric current and temperature control.
2. the nanometer environment virtual reality simulation method of molecular dynamics that places an order is characterized in that comprising the steps:
A. set up the virtual reality scenario model of unimolecule, background molecule and electrode and conducting film:
A1. make up monomolecular three-dimensional stereo model;
A2. set up the three-dimensional stereo model of liquid background and solid-state background molecule;
A3. make up the three-dimensional stereo model of electrode and conducting film;
A4. the three-dimensional stereo model of conversion structure is the data layout that Virtual Reality Modeling Language can call, and preserves;
B. set up monomolecular locus and spatial orientation model:
B1. monomolecular locus by (z) three-dimensional rectangular coordinate is determined for x, y,
Monomolecular locus coordinate can calculate according to following formula:
Wherein (x y) is the brightness of molecule hot spot in the unimolecule image, c to f
0And c
1It is scale-up factor;
B2. monomolecular spatial orientation is determined by α and two angle-datas of θ:
Monomolecular spatial orientation α value can be expressed as:
Be fluorescence light intensity on two orthogonal polarization directions that P (t) and S (t) send for unimolecule wherein, the θ angle obtains by the space asymmetry of analysis list molecular imaging speck;
C. the unimolecule luminous intensity is described:
C1. changing the single molecular fluorescence imaging device, to pass the pixel brightness value of unimolecule hot spot in the image back be unimolecule relative luminous intensity value, by calling of virtual reality applications software, and the monomolecular luminescence feature of emulation;
C2. the data of changing the acquisition of single molecular fluorescence sniffer are unimolecule relative luminous intensity value, by calling of virtual reality software, and the monomolecular luminescence feature of emulation;
C3. the unimolecule relative luminous intensity value that step c1, c2 is obtained is carried out normalized;
D. set up the motion model of unimolecule in liquid background, and the dynamic characteristic model under electric current, voltage effect;
D1. the motion model of unimolecule in liquid background; Its model can be expressed from the next:
λ wherein
xBe the root-mean-square displacement of molecule random motion, t is the time, and R is the liquid constant, and T is the absolute temperature of the physical environment of molecule, and N is an avogadros constant, and k is a coefficient of viscosity, and P is a molecular radius;
D2. the dynamic characteristic model of unimolecule under the voltage effect; The dynamic characteristic model of unimolecule under the voltage effect explained by moment, and unimolecule is as an electric dipole, and under the effect of external electric field E, suffered moment is:
Wherein q is an electric charge, and l is the direction of electric dipole moment of molecule;
D3. the dynamic characteristic model of unimolecule under the function of current; The dynamic characteristic model of unimolecule under the electric current I effect explained with the luminous intensity feature:
Wherein η is a scale-up factor, and n is a photon number,
Energy for photon;
E. realize being connected of virtual reality system and unimolecule optical detection system and molecular physics environmental parameter control system:
E1. data collecting card is gathered the data that the unimolecule optical detection system is surveyed, enter data converter, locus and spatial orientation according to molecule among the step b are described, obtain monomolecular relative position coordinates, spatial orientation data, these data save as the data file of position coordinates and spatial orientation and are called by virtual reality system;
E2. data collecting card is gathered the data that the unimolecule optical detection system is surveyed, enter data converter, describe according to monomolecular luminous intensity among the step c, obtain monomolecular relative luminous intensity data, these data save as the luminous intensity data file and are called by virtual reality system;
E3. the molecular physics ambient parameter data of virtual reality system output is stored as the ambient parameter data file, after reading and change by data converter, output to digital input-output card, connect molecular physics environmental parameter control system by data line, be used for controlling respectively electric current, voltage and the temperature of unimolecule sample physical environment;
F. realize the place an order virtual reality emulation of molecular dynamics of nanometer environment by virtual reality applications software:
Model by unimolecule, background molecule, electrode and the conducting film set up among the invocation step a, and unimolecule locus of setting up among the step b and spatial orientation model, by virtual reality applications software, realize the three-dimensional display and the various visual angles observation of unimolecule and background thereof;
By describing among step c, the d, realize the emulation of unimolecule luminance and the control of molecular physics environmental parameter.
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Cited By (8)
| Publication number | Priority date | Publication date | Assignee | Title |
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| CN103930769A (en) * | 2011-11-15 | 2014-07-16 | 马克思-普朗克科学促进协会 | Method of and apparatus for tracking a particle, particularly a single molecule, in a sample |
| US9291562B2 (en) | 2011-11-15 | 2016-03-22 | Max-Planck-Gesellschaft Zur Foerderung Der Wissenschaften E.V. | Method and apparatus for tracking a particle, particularly a single molecule, in a sample |
| CN106529187A (en) * | 2016-11-25 | 2017-03-22 | 中国科学院计算机网络信息中心 | Optimization method of embedded atom potential calculation |
| CN109726428A (en) * | 2018-11-16 | 2019-05-07 | 深圳供电局有限公司 | A kind of virtual reality electric current technique of expression |
| CN111899800A (en) * | 2020-06-12 | 2020-11-06 | 中国石油天然气股份有限公司 | Oil refining device simulation system based on molecular management technology |
| CN112233731A (en) * | 2020-10-19 | 2021-01-15 | 中山大学 | Atomic structure three-dimensional display method, atomic structure three-dimensional display system, atomic structure three-dimensional display storage medium, atomic structure three-dimensional display program, and terminal |
| CN113126773A (en) * | 2021-05-08 | 2021-07-16 | 北京理工大学 | Interactive molecular simulation system based on virtual reality technology |
| CN116740705A (en) * | 2023-04-06 | 2023-09-12 | 深圳大学 | Super-bright light spot positioning and identifying method based on random forest classification algorithm |
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| CN1782698A (en) * | 2004-11-29 | 2006-06-07 | 中国科学院大连化学物理研究所 | Method and its device for detecting molecule interaction on single molecular level |
| CN1996002A (en) * | 2006-12-22 | 2007-07-11 | 上海师范大学 | Experimental technique method for measuring unimolecular DNA conductivity |
| CN101655460A (en) * | 2009-08-28 | 2010-02-24 | 山西大学 | Method for fast optical tracking of single molecule and device thereof |
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Patent Citations (3)
| Publication number | Priority date | Publication date | Assignee | Title |
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| CN1782698A (en) * | 2004-11-29 | 2006-06-07 | 中国科学院大连化学物理研究所 | Method and its device for detecting molecule interaction on single molecular level |
| CN1996002A (en) * | 2006-12-22 | 2007-07-11 | 上海师范大学 | Experimental technique method for measuring unimolecular DNA conductivity |
| CN101655460A (en) * | 2009-08-28 | 2010-02-24 | 山西大学 | Method for fast optical tracking of single molecule and device thereof |
Cited By (11)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN103930769A (en) * | 2011-11-15 | 2014-07-16 | 马克思-普朗克科学促进协会 | Method of and apparatus for tracking a particle, particularly a single molecule, in a sample |
| US9291562B2 (en) | 2011-11-15 | 2016-03-22 | Max-Planck-Gesellschaft Zur Foerderung Der Wissenschaften E.V. | Method and apparatus for tracking a particle, particularly a single molecule, in a sample |
| CN106529187A (en) * | 2016-11-25 | 2017-03-22 | 中国科学院计算机网络信息中心 | Optimization method of embedded atom potential calculation |
| CN106529187B (en) * | 2016-11-25 | 2019-03-08 | 中国科学院计算机网络信息中心 | Embeded atom method calculation optimization method |
| CN109726428A (en) * | 2018-11-16 | 2019-05-07 | 深圳供电局有限公司 | A kind of virtual reality electric current technique of expression |
| CN111899800A (en) * | 2020-06-12 | 2020-11-06 | 中国石油天然气股份有限公司 | Oil refining device simulation system based on molecular management technology |
| CN111899800B (en) * | 2020-06-12 | 2024-05-28 | 中国石油天然气股份有限公司 | Oil refining device simulation system based on molecular management technology |
| CN112233731A (en) * | 2020-10-19 | 2021-01-15 | 中山大学 | Atomic structure three-dimensional display method, atomic structure three-dimensional display system, atomic structure three-dimensional display storage medium, atomic structure three-dimensional display program, and terminal |
| CN112233731B (en) * | 2020-10-19 | 2023-10-10 | 中山大学 | Atomic structure three-dimensional display method, system, storage medium, program, and terminal |
| CN113126773A (en) * | 2021-05-08 | 2021-07-16 | 北京理工大学 | Interactive molecular simulation system based on virtual reality technology |
| CN116740705A (en) * | 2023-04-06 | 2023-09-12 | 深圳大学 | Super-bright light spot positioning and identifying method based on random forest classification algorithm |
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