CN102063580B - 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 through 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 when measuring a large amount of unimolecule, the ensemble average signal that obtains can be covered each monomolecular characteristic, and the single-molecule detection technology can be eliminated this ensemble average experimentally.Monomolecular dynamics comprises monomolecular translation, rotation and the characteristics of luminescence etc.The single-molecule detection technology can be implemented under the nanoscale certain specific monomolecular dynamics and this unimolecule and the observation of physics environmental interaction on every side; Simultaneously optical monitoring with 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, macroscopical unimolecule of proteinase, complex and actin etc. moves.Owing to single unimolecule 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 meaning for the monomolecular probe technique 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; In virtual program software, change monomolecular physical environment parameter simultaneously, 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, unimolecule physical environment 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 unimolecule and background environment model, and to the Simulation Control of unimolecule motion and luminance; Described data transformation interface comprises data converter, data collecting card and digital input-output card; Through data line, data collecting card is connected with the unimolecule optical detection system, and digital input-output card is connected with unimolecule environmental parameter control system; Data collecting card obtains the unimolecule image of unimolecule optical detection system collection and the data of luminescence feature, gives virtual reality applications software through the data converter assignment; Simultaneously the data of unimolecule physical environment parameter in the virtual reality applications software are changed through data converter; Output to unimolecule physical environment 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, the windows window interface of this The software adopted standard comprises menu, quick botton, emulation show area, unimolecule parameter display district; Menu comprises that data file, unimolecule selection, motion control, external force controls four modules, accomplishes the read-write of unimolecule dynamics data file, monomolecular selection, the analog simulation operation of unimolecule motion and calling of unimolecule physical environment parameter control module; At the menu held function button of software interface to accomplish 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 unimolecule is selected, and follows the tracks of specific monomolecular motion; But the specific monomolecular position coordinates that unimolecule parameter display district Dynamic Display operator selectes, spatial orientation and luminous intensity information and unimolecule physical environment 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 single unimolecule luminous intensity of directly monitoring and the variation of degree of polarization.
Unimolecule physical environment 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 unimolecule, electrode and conducting film:
A1. make up monomolecular three-dimensional stereo model;
A2. set up liquid background and the monomolecular three-dimensional stereo model of solid-state background;
A3. make up electrode and the three-dimensional stereo model of conducting film in the unimolecule physical environment of living in, 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 spherical monomolecular Two dimensional Distribution;
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 confirmed for x, y, and its spatial orientation is determined by two angle-datas of α and θ:
Monomolecular locus coordinate can be confirmed according to following formula:
Wherein (x y) is the brightness of unimolecule hot spot in the unimolecule image, c to f
0And c
1Be scale-up factor, x
1And y
1It is fitting constant; Through setting the luminance threshold of unimolecule hot spot, near the certain limit the speck center, the unimolecule hot spot is carried out match with following formula, can obtain monomolecular x, y coordinate information.The information of coordinate z can obtain through the symmetry characteristic of analysis list molecule 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 through 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 normalization and is handled;
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 unimolecule random motion, t is the time, and R is the liquid constant, and T is the absolute temperature of monomolecular physical environment, and N is an avogadros constant, and k is a coefficient of viscosity, and P is the unimolecule 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 unimolecule electric dipole moment.Can find out that thus the electric field force that the unimolecule of different spaces orientation receives 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 different monomolecular orientations.
D3. set up the physical model that the luminescence feature of unimolecule under the function of current changes.The luminescence feature model of unimolecule under the function of current can be expressed as:
Wherein η is a scale-up factor, has different scale-up factors for different unimolecules, and it can obtain through the experimental data match; N is luminous photon number, and
is the energy of photon.According to law of conservation of energy, when electric current I process unimolecule, current changing rate equals the variation of single molecular fluorescence.
Monomolecular fluorescence produces owing to electronics transits to ground state spontaneous radiation process from excited state.Under the function of current, electronics in the unimolecule and outer field current generation electron exchange.The probability size that the excited state electronics is transferred in the size decision unimolecule of electric current, thus unimolecule spontaneous radiation change of luminous intensity caused.
E. realize being connected of virtual reality system and unimolecule optical detection system and unimolecule physical environment parameter control system:
E1. data collecting card is gathered the data that the unimolecule optical detection system is surveyed; Get into data converter; Describe according to monomolecular locus and spatial orientation among the step b; 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; Get into data converter; Describe according to monomolecular luminous intensity among the step c, obtain monomolecular relative luminous intensity value, these data save as the data file of luminous intensity values and are called by virtual reality system;
E3. the unimolecule physical environment supplemental characteristic 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 unimolecule physical environment parameter control system through 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 through 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, unimolecule parameter display district; Menu comprises that data file, unimolecule selection, motion control, external force controls four modules, accomplishes the read-write of unimolecule dynamics data file, monomolecular selection, the analog simulation operation of unimolecule motion and calling of unimolecule physical environment parameter control module;
F2. the model of unimolecule, background unimolecule, electrode and the conducting film through 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 through calling the data file of unimolecule 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 through data-interface.
Compared with prior art, the present invention has realized the place an order virtual reality emulation of molecular motion state and luminescence feature of nanometer environment, can the unimolecule dynamic characteristic of nanoscale be showed visually.In virtual reality scenario, realized through changing unimolecule physical environment parameter controlling to the unimolecule dynamic process.Through 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 property and the illustrative of virtual reality technology in research nanometer unimolecule 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 monomolecular 3-d modelling figure of Fig. 2 Cy5 fluorescent dye
The monomolecular 3-D solid structure model of Fig. 3 glycerine
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 fluorescent dye unimolecule 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 (like 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; Unimolecule physical environment 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; Through calling the data of data transformation interface; Analog simulation unimolecule dynamic characteristic, and realize the emulation of unimolecule dynamic characteristic is controlled through changing unimolecule physical environment parameter;
Unimolecule physical environment control system 3 comprises: voltage, electric current and temperature control equipment, and unimolecule physical environment control module 4 is connected through 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 through 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 specifies with the Cy5 unimolecule:
A. set up the monomolecular virtual reality scenario model of unimolecule and background, comprising:
A1. according to the chemical constitution of Cy5 molecule, utilize chemical simulation configuration software Culgi to make up the three-dimensional stereo model of Cy5 molecule, shown in Figure 2 is the monomolecular three-dimensional stereo model of Cy5 fluorescent dye;
A2. utilize chemical simulation configuration software Culgi to make up liquid background (glycerine unimolecule; Like Fig. 3) and solid-state background (the big molecule of PMMA organic long-chain; Like Fig. 4) the unimolecule three-dimensional stereo model, re-use and play up and make software 3dmax based on the three-dimensional animation of PC system and design above-mentioned unimolecule simplified models three-dimensional stereo model;
A3. use based on the three-dimensional animation of PC system and play up and make electrode and the model of conducting film in the software 3dmax design unimolecule physical environment of living in; 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 spherical monomolecular Two dimensional Distribution, 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 (like Fig. 5), it at three-dimensional relative position by (z) three-dimensional rectangular coordinate is confirmed for x, y, and its spatial orientation is determined by two angle-datas of α and θ.
Monomolecular locus coordinate can calculate according to following formula:
Wherein (x is that (x y) locates the brightness of unimolecule hot spot, c to coordinate in the unimolecule image y) 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 characteristics 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 through the following formula match; The information of coordinate z can obtain through the symmetry characteristic of analysis list molecule 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 through the space asymmetry of analysis list molecular imaging hot spot;
B2. set up the relative position relation between unimolecule and the background unimolecule: unimolecule immerses in the liquid glycerin unimolecule; On the big molecule long-chain of list of unimolecule attached to solid-state background surface, along with single 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. reading the signal that the single molecular fluorescence sniffer obtains, is unimolecule relative luminous intensity value with data-switching, is 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 the normalization processing;
D. set up the motion model of unimolecule in liquid background unimolecule, and the dynamic characteristic model under the electric current, voltage effect:
D1. set up the motion model of unimolecule in liquid background unimolecule; Its model can be expressed from the next:
λ wherein
xBe the root-mean-square displacement of unimolecule random motion, t is the time, and R is the liquid constant, and T is the absolute temperature of monomolecular physical environment, and N is an avogadros constant, and k is a coefficient of viscosity, and P is the unimolecule radius.In the liquid background unimolecule under disturb in no outfield, the description of following formula is obeyed in the monomolecular random motion of unimolecule and liquid background.
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 unimolecule electric dipole moment.Can find out that thus the electric field force that the unimolecule of different spaces orientation receives 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 different monomolecular orientations.
D3. set up the physical model that the luminescence feature of unimolecule under the function of current changes.The luminescence feature model of unimolecule under the function of current can be expressed as:
Wherein η is a scale-up factor, has different scale-up factors for different unimolecules, and it can obtain through the experimental data match; N is the photon number of spontaneous transition, and
is the energy of spontaneous transition photon.According to law of conservation of energy, when electric current I process unimolecule, current changing rate equals the variation of single molecular fluorescence.
Monomolecular fluorescence 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 unimolecule and electric current generation electron exchange, the probability that the excited state electronics is transferred in the size decision unimolecule of electric current, thus cause unimolecule spontaneous radiation change of luminous intensity.
E. realize being connected of virtual reality system and unimolecule physical environment control system and unimolecule optical detection system:
E1. data collecting card is gathered the data that the unimolecule optical detection system is surveyed; Get into data converter; Describe according to monomolecular relative position coordinates and spatial orientation among the step b; 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; Get into data converter; According to single monomolecular luminance model among the step c, obtain monomolecular relative luminous intensity value, these data save as the luminous intensity data file and are called by virtual reality system;
E3. the unimolecule physical environment supplemental characteristic 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 unimolecule physical environment parameter control system through 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 is as shown in Figure 8;
F1. utilize virtual reality to develop software and design the human-computer interaction interface of virtual reality applications software, the windows window interface of this The software adopted standard comprises menu, quick botton, emulation show area, unimolecule parameter display district; Menu comprises that data file, unimolecule selection, motion control, external force controls four modules, accomplishes the read-write of unimolecule dynamics data file, monomolecular selection, the analog simulation operation of unimolecule motion and calling of unimolecule physical environment parameter control module; At the menu held function button of software interface to accomplish 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 unimolecule is selected, and follows the tracks of specific monomolecular motion; But the specific monomolecular position coordinates that unimolecule parameter display district Dynamic Display operator selectes, spatial orientation and luminous intensity information and unimolecule physical environment parameter information;
F2. the model of unimolecule, background unimolecule, electrode and the conducting film through 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 observes with various visual angles, use mouse or keyboard can adjust viewing angle; The unimolecule choice menus realizes calling different unimolecule models, background unimolecule model;
F3. the virtual reality system application software realizes the emulation of unimolecule translation, rotary state and luminance through calling the data file of unimolecule 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 liquid glycerin unimolecule 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 unimolecule parameter display district, 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 unimolecule 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 outputed to data transformation interface simultaneously, are connected with voltage-operated device through digital input-output card, realize controlling reality is monomolecular;
Design unimolecule current control module is used the electric current of mobile electronic model emulation through conducting film, and the adjusting of size of current realizes with slide block; And the current switch of design mouse control, realizing current switch and size adjustment, the data of electric current show in unimolecule parameter display district; According to the dynamic effect of 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, and 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 that adds on three electrodes is different; Unimolecule demonstrates 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 unimolecule parameter display district, according to the variation of the descriptive model emulation unimolecule in the steps d 1 with the motion state that temperature variation produced; 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, unimolecule physical environment 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; Through data line, data collecting card is connected with the unimolecule optical detection system, and digital input-output card is connected with unimolecule environmental parameter control system; Data collecting card obtains the unimolecule image of unimolecule optical detection system collection and the data of luminescence feature, gives virtual reality applications software through the data converter assignment; The data of unimolecule physical environment parameter are changed through data converter in the virtual reality applications software; Output to unimolecule physical environment parameter control system by digital input-output card; Be used for controlling respectively monomolecular physical environment parameter, comprise electric current, voltage and temperature;
The windows window interface of described virtual reality applications The software adopted standard comprises menu, emulation show area, unimolecule parameter display district; Menu comprises that data file, Molecular Selection, motion control, external force controls four modules, accomplishes the read-write of unimolecule dynamics data file, monomolecular selection, the analog simulation operation of unimolecule motion and calling of unimolecule physical environment 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 unimolecule, follows the tracks of specific monomolecular motion; But the specific monomolecular volume coordinate that unimolecule parameter display district Dynamic Display operator selectes, spatial orientation and luminous intensity information and unimolecule physical environment parameter information;
Described unimolecule optical detection system comprises 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;
Described unimolecule physical environment parameter control system comprises voltage, electric current and temperature control equipment, can be respectively to unimolecule physical environment 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 liquid background and the monomolecular three-dimensional stereo model of solid-state background;
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 confirmed for x, y,
Monomolecular locus coordinate can calculate according to following formula:
Wherein (x y) is the brightness of unimolecule hot spot in the unimolecule image, c to f
0And c
1Be scale-up factor, x
1And y
1It is fitting constant; Through setting the luminance threshold of unimolecule hot spot, near the certain limit the speck center, the unimolecule hot spot is carried out match with following formula; Can obtain monomolecular x, y coordinate information, the information of coordinate z can obtain through the symmetry characteristic of analysis list molecule hot spot;
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 through 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, through 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, through 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 normalization and is handled;
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 unimolecule random motion, t is the time, and R is the liquid constant, and T is the absolute temperature of monomolecular physical environment, 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 is through the moment statement, 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 unimolecule electric dipole moment;
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 characteristic:
Wherein η is a scale-up factor; N is a photon number, and
is the energy of photon;
E. realize being connected of virtual reality system and unimolecule optical detection system and unimolecule physical environment parameter control system:
E1. data collecting card is gathered the data that the unimolecule optical detection system is surveyed; Get into data converter; Describe according to monomolecular locus and spatial orientation among the step b; 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; Get into data converter; Describe according to monomolecular luminous intensity among the step c, obtain monomolecular relative luminous intensity value, these data save as the luminous intensity data file and are called by virtual reality system;
E3. the unimolecule physical environment supplemental characteristic 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 unimolecule physical environment parameter control system through 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 through virtual reality applications software:
Model through 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; Through virtual reality applications software, realize the three-dimensional display and various visual angles observation of unimolecule and background thereof;
Through describing among step c, the d, realize the emulation and the unimolecule physical environment parameter control of unimolecule luminance.
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| DE102011055367B4 (en) * | 2011-11-15 | 2017-02-09 | MAX-PLANCK-Gesellschaft zur Förderung der Wissenschaften e.V. | Method and device for tracking a movement of a particle, in particular 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 |
| 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 |
| CN112233731B (en) * | 2020-10-19 | 2023-10-10 | 中山大学 | Atomic structure three-dimensional display method, system, storage medium, program, and terminal |
| CN113126773B (en) * | 2021-05-08 | 2023-05-30 | 北京理工大学 | Interactive molecular simulation system based on virtual reality technology |
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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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| 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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