JP4369783B2 - Hardware simulator - Google Patents

Description

  The present invention relates to a hardware simulator that is configured from predetermined hardware and that simulates the amount of change of a simulation object due to a reaction between simulation objects.

  As a conventional chemical reaction simulation method, for example, by executing a simulation program on a computer, a finite temperature and a finite time are set, a molecular dynamics calculation at the finite temperature and a finite time is performed, and a molecular dynamics calculation is performed. In some cases, all of the structures including excited states are used to obtain a plurality of stable structures in which all the forces acting on all atoms of the substance are alleviated (see Patent Document 1).

On the other hand, in order to easily handle a large number of substances in the chemical reaction simulation as described above, the present inventor has proposed that the chemical reaction simulation is performed using predetermined hardware. In this case, A reaction execution circuit is provided for each chemical reaction, and simulation is performed by increasing or decreasing the value of each substance counter by this reaction execution circuit (see Patent Document 2).
JP 2002-260975 A JP 2002-126497 A

  However, if each circuit is configured so as to be able to cope with all events, the circuit configuration becomes too complex and the simulation time also increases. In particular, when each circuit is configured so as to be able to cope with an event that occurs rarely, the above-mentioned tendency becomes remarkable, and the device cost becomes enormous. In addition, if an event that occurs rarely is handled manually, the simulation is interrupted for a long time, and the simulation time further increases.

  An object of the present invention is to provide a hardware simulator capable of correcting a device configuration so as to automatically cope with an event that rarely occurs without complicating the circuit configuration. It is.

  A hardware simulator according to the present invention is a hardware simulator configured from predetermined hardware and simulating a change amount of a simulation target object due to a reaction between the simulation target objects. An arithmetic element, a plurality of reaction circuits that change the value of the arithmetic element according to a reaction between the simulation objects, and a connection between the reaction circuit and the arithmetic element according to a reaction between the simulation objects It is determined whether or not a predetermined correction condition is satisfied based on the switching circuit and the value of the arithmetic element, and when it is determined that the correction condition is satisfied, the operation of the apparatus is stopped and the reaction circuit and the The reaction circuit is controlled by controlling the switching circuit so as to change a connection state with the arithmetic element. After modifying the connection state between said operation elements, in which and a correction means for resuming the operation of the device.

  In the hardware simulator according to the present invention, the values of a plurality of computing elements that calculate values related to the simulation object are changed by the reaction circuit in accordance with the reaction between the simulation objects, thereby simulating the reaction between the simulation objects. The amount of change of the object is simulated. At this time, it is determined whether or not a predetermined correction condition is satisfied based on the value of the arithmetic element, and when it is determined that the correction condition is satisfied, the connection state between the reaction circuit and the arithmetic element is changed. After the connection state between the reaction circuit and the computing element is corrected by controlling the circuit, the operation of the apparatus is resumed. Therefore, an event that occurs rarely is detected as a correction condition, and a new event that occurs as a result of this event is detected. It is possible to correct the connection state between the reaction circuit and the computing element so that a simple reaction can be processed, and it is possible to automatically deal with an event that rarely occurs without complicating the circuit configuration. Thus, the device configuration can be modified.

  The computing element is provided for each group obtained by grouping a plurality of second simulation objects assigned to the first simulation object and reacting with the first simulation object. A plurality of counting circuits for counting values related to the object, wherein the reaction circuit reduces the count value of the counting circuit representing the amount of each simulation object before the reaction according to the progress of the reaction, and after the reaction It is preferable to increase the count value of the count circuit representing the amount of each simulation object.

  In this case, even when there are many second simulation objects that react with the first simulation object, the second simulation objects are grouped, and the count circuit of the first simulation object is individually provided for each group. Therefore, it is possible to reduce the number of count circuits of the second simulation object to be connected to the count circuit of the first simulation object, and to easily wire between the count circuit and the reaction circuit. can do.

  The correction means determines whether the count value of one count circuit among the plurality of count circuits has reached a predetermined lower limit value as the correction condition, and the count value of the one count circuit is set to a lower limit value If it is determined that the number of connections has been reached, the operation of the apparatus is stopped, and the reaction circuit that increases the one count circuit and the number of connections between the one count circuit and the other count circuit are increased. It is preferable to include a correction circuit that restarts the operation of the apparatus after the connection state between the reaction circuit and the count circuit is corrected by controlling the switching circuit so that the number of connections increases.

  In this case, when the correction circuit causes the count value of one of the plurality of count circuits to reach a predetermined lower limit value and becomes smaller than the count value of the other count circuit, the operation of the device is stopped, The switching circuit is controlled so that the number of connections between the reaction circuit that increases the count circuit and one count circuit is greater than the number of connections between the reaction circuit that increases the other count circuit and the other count circuit, and the reaction circuit counts. Since the operation of the device is resumed after correcting the connection state with the circuit, the connection state between the reaction circuit and the count circuit so that the count value of the count circuit whose count value has decreased is higher than that of other count circuits Can be corrected automatically.

  The correction means determines whether the count value of one count circuit among the plurality of count circuits has reached a predetermined upper limit value as the correction condition, and sets the count value of the one count circuit to an upper limit value. When it is determined that the number of connections has been reached, the operation of the apparatus is stopped, and the reaction circuit that reduces the one count circuit and the number of connections between the one count circuit and the other count circuit are reduced. It is preferable to include a correction circuit that restarts the operation of the apparatus after the connection state between the reaction circuit and the count circuit is corrected by controlling the switching circuit so that the number of connections increases.

  In this case, the correction circuit stops the operation of the device when the count value of one count circuit among the plurality of count circuits reaches the upper limit value and becomes larger than the count value of the other count circuit. The switching circuit is controlled so that the number of connections between the reaction circuit that reduces the number of the reaction circuit and one count circuit is larger than the number of connections between the reaction circuit that reduces the other count circuit and the other count circuit, Since the operation of the device is resumed after correcting the connection state of the counter, the connection state between the reaction circuit and the count circuit is automatically adjusted so that the count value of the count circuit whose count value has increased is smaller than that of other count circuits. Can be corrected.

  The correcting means may be composed of a host computer. In this case, the above correction process can be performed using a general-purpose host computer.

  According to the present invention, it is determined whether or not a predetermined correction condition is satisfied based on the value of the arithmetic element, and when it is determined that the correction condition is satisfied, the connection state between the reaction circuit and the arithmetic element is changed. After controlling the switching circuit to correct the connection state between the reaction circuit and the computing element, the operation of the apparatus is resumed, so that an event that rarely occurs is detected as a correction condition. The connection state between the reaction circuit and the computing element can be modified so that a new reaction that occurs as a result can be processed, and an event that rarely occurs is automatically handled without complicating the circuit configuration. The device configuration can be modified so that it is possible.

  Hereinafter, as an example of a hardware simulator according to the present invention, a chemical reaction simulation apparatus that simulates a biochemical reaction and is suitably used for elucidating a signal transmission network, a gene network, and the like will be described with reference to the drawings.

  FIG. 1 is a block diagram showing a configuration of a hardware simulator according to an embodiment of the present invention. The hardware simulator shown in FIG. 1 includes a plurality of random number generators R1 to Rn (n is an arbitrary positive number), a plurality of enzyme counters K1 to Kn, a plurality of throttle circuits V1 to Vn, and a plurality of reaction execution circuits H1 to Hn. A plurality of substance counters B1 to Bm (m is an arbitrary positive number), a connection switching circuit SW, and a connection change control unit CC.

  The enzyme counters K1 to Kn, the throttle circuits V1 to Vn, and the reaction execution circuits H1 to Hn are provided for each biochemical reaction used for the simulation. For example, the substance counters B1 to B3 are one substance used for the simulation. The material counters B4 to Bm are provided for each of the other materials used for the simulation. At this time, a plurality of substances that react with one substance are grouped, and substance counters B1 to B3 are provided for each group. The method of assigning each substance to the substance counters B1 to Bm is not particularly limited to the above example, and one substance is divided and assigned to two or less substance counters or four or more substance counters. Various changes, such as dividing and assigning to a plurality of substance counters, are possible.

  The random number generator R1 is connected to the input side of the aperture circuit V1, the reaction execution circuit H1 is connected to the output side of the aperture circuit V1, and the enzyme counter K1 is connected to the aperture circuit V1. Other random number generators, enzyme counters, throttle circuits, and reaction execution circuits are also connected in the same manner as described above.

  The connection switching circuit SW is composed of, for example, a space switch or the like, and includes a plurality of increase command input wires I1 to In and a decrease command input wires D1 to Dn, and a plurality of increase command output wires i1 to im. The output wirings d1 to dm for reduction command are included, and each wiring is arranged in a matrix.

  The reaction execution circuit H1 is connected to the input wiring I1 for increase command and the input wiring D1 for decrease command of the connection switching circuit SW, and other reaction execution circuits are similarly connected. The substance counter B1 is connected to the output wiring i1 for increase command and the output wiring d1 for decrease command of the connection switching circuit SW, and other substance counters are similarly connected. In the connection switching circuit SW, a switch (not shown) including a time-division gate and a holding memory for controlling on / off of the time-division gate is arranged at the intersection ND of each wiring indicated by a black circle in the drawing. ing.

  The connection switching circuit SW turns on / off each switch to connect the increase command input wires I1 to In to the increase command output wires i1 to im and decrease command input wires D1 to Dn. Controls the connection state with the output wirings d1 to dm for the decrease command, and corresponds to the substance counter representing the substance before the reaction of the biochemical reaction represented by each reaction execution circuit H1 to Hn and the substance counter representing the substance after the reaction. Connect the reaction execution circuit. The connection switching circuit SW is not particularly limited to the above space switch, and other connection switching circuits may be used as long as the connection state between the reaction execution circuit and the substance counter can be switched.

  The substance counters B1 to Bm are composed of binary counters and the like. For example, the substance counters B1 to B3 initially count the number of one substance before the reaction or after the reaction, that is, a predetermined number of molecules or atoms, respectively. The substance counters B4 to Bm are set with the number of other substances before or after the reaction, that is, the number of molecules or the number of atoms as the initial count value. The substance counters B1 to Bm decrease and increase the count values according to the decrease command and the increase command of the reaction execution circuits H1 to Hn. Further, the substance counters B1 to Bm output their count values to the connection change control unit CC.

  Note that the substance counter is not particularly limited to the binary counter described above, and any other counter or the like may be used as long as it is an arithmetic element that is provided for the simulation target and calculates a value related to the simulation target. For example, when a biochemical reaction such as a citric acid circuit in a metabolic pathway is regarded as a state transition and used in combination with a state transition machine (finite state automaton), a Johnson counter is used as a substance counter, thereby enabling a faster and more compact circuit. Can be simulated.

  The random number generator R1 outputs a predetermined random number for controlling the reaction rate of the biochemical reaction to the reaction execution circuit H1 via the throttle circuit V1. As the random number generator, a pseudo random number generation circuit that generates pseudo random numbers, a chaos generation circuit that generates chaotic random numbers, a thermal noise generation circuit that generates random numbers based on thermal noise, and the like can be used.

For example, as a pseudo-random number generation circuit, a linear feedback shift register is used, and when the linear feedback shift register is composed of L registers, a random number having a long period of 2 ^L -1 is generated. Can be made. As the chaos generation circuit, an irregular random number that performs chaotic behavior can be generated by using a circuit that generates an irregular signal by a closed loop including a capacitor and a variable resistance circuit. As a thermal noise generation circuit, by using a circuit that latches short cycle pulses with long cycle pulses and outputs the level of the latched short cycle pulses as random numbers, random numbers without periodicity due to white noise can be generated. Can be generated.

  The enzyme counter K1 is set with the number of enzyme substances used in the biochemical reaction represented by the reaction execution circuit H1, that is, the number of molecules of the enzyme substance as its count value, and the aperture of the aperture circuit V1 according to the set count value. The amount is adjusted. In the case of a general chemical reaction, the enzyme counter is changed to a catalyst counter, and the number of catalytic substances is set as the count value instead of an enzyme that is a protein biocatalyst produced in living cells. In the case of a chemical reaction that does not use a catalyst (enzyme), a catalyst (enzyme) counter and a throttle circuit are not required.

  Specifically, the random number generator R1 randomly generates “1” or “0” data as a random number, and the enzyme counter K1 adjusts the frequency of “1” with respect to “0” according to the count value. Data of “1” or “0” is output. At this time, the aperture circuit V1 takes the logical product of both data and outputs the result to the reaction execution circuit H1. Therefore, the frequency of “1” input to the reaction execution circuit H1 is adjusted according to the count value of the enzyme counter K1.

  When “1” is input as data, the reaction execution circuit H1 outputs an increase command for increasing the count value by 1 to the increase command input wiring I1 and executes a decrease command. A decrease command for decreasing the count value by 1 is output to the input wiring D1. On the other hand, when “0” is input as data, the reaction execution circuit H1 does not output an increase command and a decrease command so as not to perform a reaction (non-execution state).

  At this time, the connection switching circuit SW is connected to the input wiring D1 for decrease command and the substance counter representing the number of substances before reaction in the biochemical reaction represented by the reaction execution circuit H1, that is, the number of molecules or the number of atoms. The output wiring for the reduction command is connected. Therefore, the decrease command output from the reaction execution circuit H1 is input to the substance counter provided for the substance before the reaction, and the substance counter decreases its count value by one. The connection switching circuit SW is connected to an increase command input wiring I1 and a substance counter representing the number of substances after reaction in the biochemical reaction represented by the reaction execution circuit H1, that is, the number of molecules or the number of atoms. The output wiring for command is connected. Therefore, the increase command output from the reaction execution circuit H1 is input to the substance counter provided for the substance after the reaction, and the substance counter increases its count value by one.

  Other random number generators, enzyme counters, throttling circuits, and reaction execution circuits are also configured in the same manner as described above, and operate in the same manner as described above according to biochemical reactions. When the number of enzymes assigned to the enzyme counter increases or decreases due to a biochemical reaction or the like, the enzyme counter is also configured in the same way as the substance counter and is connected to the connection switching circuit, and the count value is increased or decreased by the corresponding reaction execution circuit. Is done.

  The connection change control unit CC is composed of a predetermined logic circuit and the like, and by controlling the on / off of each switch of the connection switching circuit SW, the increase command input wirings I1 to In and the increase command output wiring i1. To im, and the connection state between the input wirings D1 to Dn for reduction command and the output wirings d1 to dm for reduction command are changed. The connection change control unit CC determines whether or not a predetermined correction condition is satisfied based on the count values of the substance counters B1 to Bm, and when determining that the correction condition is satisfied, stops the operation of the apparatus. After controlling the connection switching circuit SW so as to change the connection state between the reaction execution circuits H1 to Hn and the substance counters B1 to Bm and correcting the connection state between the reaction execution circuits H1 to Hn and the substance counters B1 to Bm, Resume device operation.

  For example, the connection change control unit CC acquires the count values of the substance counters B1 to B3 assigned to one substance, and the count value of one substance counter among the substance counters B1 to B3 is a lower limit as a correction condition. Determine if the value has been reached. When it is determined that the count value of one substance counter has reached the lower limit value, the connection change control unit CC outputs a stop signal SS for stopping the operation of the device to each unit to stop the operation of the device. The number of connections between the reaction execution circuit that increases the count value of one substance counter and the one substance counter is larger than the number of connections between the reaction execution circuit that increases the other substance counter and the other substance counter. The connection state of the connection switching circuit SW is switched, and then a restart signal RS for restarting the operation of the apparatus is output to each unit to restart the operation of the apparatus and continue the simulation operation.

  Further, the connection change control unit CC determines whether or not the count value of one substance counter among the substance counters B1 to B3 has reached the upper limit value as the correction condition. When it is determined that the count value of one substance counter has reached the upper limit value, the connection change control unit CC outputs a stop signal SS for stopping the operation of the device to each unit and stops the operation of the device. The number of connections between the reaction execution circuit that decreases the count value of one substance counter and the one substance counter is greater than the number of connections between the reaction execution circuit that decreases the other substance counter and the other substance counter. The connection state of the connection switching circuit SW is switched, and then a restart signal RS for restarting the operation of the apparatus is output to each unit to restart the operation of the apparatus and continue the simulation operation.

  For example, when the substance counters B1 to B3 are composed of 6-bit counts and the count range is 0 to 63, 5 is the lower limit value, 58 is the upper limit value, and the count values of the substance counters B1 to B3 are the lower limit value or the upper limit value. Reaching the value is the correction condition. The number of bits of the substance counter is not particularly limited to the above example, and various changes can be made. Also, the correction condition is not particularly limited to the above example, and various conditions can be used as the correction condition as long as the conditions are predetermined such as various events that rarely occur. Further, the substance counter managed by the connection change control unit CC is not particularly limited to the above example, and the connection value between the other substance counter and the reaction execution circuit is changed by managing the count value of the other substance counter. Also good. For example, when the count value of one substance counter assigned to one substance reaches the upper limit value, various changes such as changing the connection state with the reaction execution circuit by dividing the substance counter into two or more Is possible.

  In the present embodiment, the substance counters B1 to Bm correspond to examples of arithmetic elements and count circuits, and the reaction execution circuits H1 to Hn, the random number generators R1 to Rn, the enzyme counters K1 to Kn, and the throttling circuits V1 to Vn react. The connection switching circuit SW corresponds to an example of a switching circuit, and the connection change control unit CC corresponds to an example of a correction unit and a correction circuit.

  Next, the operation of the hardware simulator configured as described above will be described. First, using necessary data on the substance to be simulated, biochemical reaction, enzyme, etc., the substance counters B1 to B3 are distributed and set so that the sum of these initial values represents the number of one substance. The initial value of the counter indicating the number of each substance is set in the substance counters B4 to Bm, and the initial value of the counter indicating the number of each enzyme is set in the enzyme counters K1 to Kn. Next, the random number generators R1 to Rn generate the above random numbers, and the diaphragm circuits V1 to Vn correct the random numbers according to the number of enzymes in the enzyme counters K1 to Kn. The reaction execution circuits H1 to Hn set the count values of the substance counters B1 to Bm representing the number of molecules or atoms of the substance before the reaction to 1 so that the reaction is executed according to the random number value corrected by the number of enzymes. And the count value of the substance counters B1 to Bm indicating the number of molecules or atoms of the substance after the reaction is increased by one.

  In this way, the reaction rate of the biochemical reaction represented by each reaction execution circuit H1 to Hn is adjusted for each reaction execution circuit H1 to Hn, and the substances before and after the reaction of the biochemical reaction represented by each reaction execution circuit H1 to Hn are adjusted. The corresponding substance counters B1 to Bm are connected to the corresponding reaction execution circuits H1 to Hn, and the substance counters B1 to Bm corresponding to the substances before and after the reaction according to the biochemical reaction represented by each reaction execution circuit H1 to Hn. The count value is decreased or increased and multiple biochemical reactions are simulated in parallel.

  In this way, since the amount of each substance before and after the reaction is regarded as a count value, that is, a number (integer), and the amount of change of the substance due to the biochemical reaction is simulated, only the number of substance counters B1 to Bm is increased. The types of substances used for simulation can be increased. In addition, even when an unknown biochemical reaction is newly found, a new biochemical reaction or deficiency is detected even if a biochemical reaction is deficient due to a disease etc. This can be easily dealt with by changing the connection state between the reaction execution circuits H1 to Hn and the substance counters B1 to Bm by the connection switching circuit SW according to the biochemical reaction performed and the biochemical reaction different from normal.

  Here, the substance counters B1 to B3 are provided for one substance, and a plurality of substances that react with the one substance are grouped and provided for each group. FIG. 2 is a schematic diagram for explaining a method of correcting the connection state according to the count value of the substance counter. The direction of the arrow in the figure indicates the reaction direction, and the value of the substance counter on the start point side of the arrow decreases according to the reaction, and the value of the substance counter on the end point side of the arrow increases.

  For example, when a certain substance b0 reacts with 15 substances of seven substances x1 to x7, three substances y1 to y3, and five substances z1 to z5, it is shown in FIG. Thus, 15 substances x1 to x7, y1 to y3, z1 to z5 are divided into three groups of seven substances x1 to x7, three substances y1 to y3, and five substances z1 to z5. The material is divided into groups, and material counters B1 to B3 for the material b0 are provided for each group. The substance counter B1 is connected to seven substance counters X1 to X7 (seven substance counters among the substance counters B4 to Bm shown in FIG. 1), and the substance counter B2 is connected to three substance counters Y1 to Y3 (FIG. 1 is connected to three substance counters B4 to Bm shown in FIG. 1, and the substance counter B3 is five substance counters Z1 to Z5 (five substance counters among the substance counters B4 to Bm shown in FIG. 1). ).

  During the above simulation, when the count value of the substance counter B3 reaches the lower limit “5” and the count values of the substance counters B1 and B2 reach 44 and 49, the connection change control unit CC After determining that the count value of B3 has reached the lower limit and outputting a stop signal SS for stopping the operation of the apparatus to each part, the number of arrows input to the material counter B3 increases, and the material counter with a large count value The connection state of the connection switching circuit SW is switched so that the arrow output from B2 increases. As a result, as shown in FIG. 2B, the connection switching circuit SW is connected so that the arrow from the substance counter Y3 is input to the substance counter B3 and the arrow from the substance counter B2 is input to the substance counter Z2. After the state is switched, the connection change control unit CC outputs a restart signal RS for restarting the operation of the device to each unit to restart the operation of the device and continue the simulation operation.

  The connection state correction process by the connection change control unit CC can also be realized by the host computer executing a predetermined correction program. In this case, the above correction process is performed using a general-purpose host computer. Can be done automatically.

  As described above, in the present embodiment, it is determined whether the count value of one substance counter among the substance counters B1 to B3 has reached the lower limit value or the upper limit value as the correction condition, and the count of one substance counter is determined. When it is determined that the value has reached the lower limit value or the upper limit value, the substance counter and the reaction execution circuit are set so that the count value of the substance counter that has reached the lower limit value or the upper limit value returns to the intermediate value after the operation of the apparatus is stopped. Since the operation of the device is resumed after correcting the connection state with the substance, the substance assigned to the substance is maintained while maintaining the overall reaction network for one substance without complicating the circuit configuration. The device configuration can be automatically corrected so that the count value of the counter is within an appropriate range. Even when there are many other substances that react with one substance, the other substances are divided into groups, and the substance counters B1 to B3 for one substance are provided for each group. The number of substance counters to be connected to B3 can be reduced, and wiring between the substance counters B1 to B3 and the reaction execution circuit can be easily performed.

  Next, a case where a biochemical reaction in a cell is simulated in consideration of a concentration gradient of each substance in the cell will be described. FIG. 3 is a schematic diagram for explaining a method of simulating a biochemical reaction in a cell in consideration of a concentration gradient of each substance in the cell.

  As shown in FIG. 3, when simulating a biochemical reaction in a cell, one cell is divided into a plurality of cells CE, the amount of the substance is held for each cell CE, and the concentration gradient of each substance is obtained by a cellular automaton. To simulate. That is, the diffusion of each substance between cells is simulated from the concentration (amount) of each substance in the target cell and the concentrations (amounts) of substances in the six neighboring cells.

  For example, when two adjacent cells C1 and C2 contain substances 1, 2 and 3 having different concentrations, each substance diffuses from the higher concentration to the lower cell C1 and C2. The diffusion between the cells can be simulated as follows.

  FIG. 4 is a block diagram showing a configuration of a hardware simulator in the case of simulating the diffusion of substances in the two cells shown in FIG. The hardware simulator shown in FIG. 4 includes a hardware simulator CB1 for the cell C1, a hardware simulator CB2 for the cell C2, and a diffusion circuit KC.

  The total value of the count values of the substance counters B1a to B1c in the hardware simulator CB1 shown in FIG. 4 represents the number of molecules or atoms of the substance 1 in the cell C1, and each count value of the substance counters B2 and B3 This represents the number of molecules or atoms of substances 2 and 3 in C1, and the total value of the substance counters B1a 'to B1c' in hardware simulator CB2 represents the number of molecules or atoms of substance 1 in cell C2. Each of the counter values of the substance counters B2 ′ and B3 ′ represents the number of molecules or atoms of the substances 2 and 3 in the cell C2, and each of the substance counters B1a to B3 and B1a ′ to B3 ′ includes the diffusion circuit KC. Connected through. The connection change control unit CC changes the connection state of the connection switching circuit (not shown) according to the count values of the substance counters B1a to B1c, and the connection change control unit CC ′ counts the count values of the substance counters B1a ′ to B1c ′. The connection state of the connection switching circuit (not shown) is changed accordingly.

  The diffusion circuit KC includes substance counters B1a to B3, B1a 'to B3 so that each substance diffuses according to the count values of the substance counters B1a to B3, B1a' to B3 ', that is, the number of molecules or atoms of each substance. Control the count value of '. For example, when the total value of the count values of the substance counters B1a to B1c is larger than the total value of the count values of the substance counters B1a ′ to B1c ′, the counts of the substance counters B1a to B1c are followed according to a predetermined diffusion rate until an equilibrium state is reached. The values are sequentially decreased, and the count values of the substance counters B1a ′ to B1c ′ are sequentially increased correspondingly.

  In FIG. 4, only the connection change control units CC and CC ′ and the material counters B1a to B3 and B1a ′ to B3 ′ are illustrated in the hardware simulators CB1 and CB2 for the cells C1 and C2. The simulators CB1 and CB2 are also configured in the same manner as the hardware simulator shown in FIG. 1, and have a random number generator, an enzyme counter, a throttle circuit, a reaction execution circuit, and a connection switching circuit (not shown). Accordingly, the hardware simulators CB1 and CB2 also operate in the same manner as the hardware simulator shown in FIG. 1, and the internal biochemical reaction is simulated for each of the cells C1 and C2, and the substance counters B1a to B1c and B1a ′ to B1c ′. When the count value of one of the substance counters reaches the lower limit value or the upper limit value, the connection change control unit CC stops the operation of the entire apparatus, and the count value of the substance counter that has reached the lower limit value or the upper limit value is intermediate. After correcting the connection state between the substance counter and the reaction execution circuit so as to return to the value, the operation of the apparatus is resumed.

  As described above, the cell is divided into a plurality of cells, and the amount of change of the substance due to the biochemical reaction is simulated for each cell, and each substance in the cell is simulated by simulating the diffusion of each substance between adjacent cells. The change amount of the substance in the cell can be simulated in consideration of the substance concentration gradient. At the same time, it is determined as a correction condition that the count value of one of the substance counters B1a to B1c and B1a ′ to B1c ′ is the lower limit value or the upper limit value. In this case, the operation of the apparatus is stopped, While maintaining the overall reaction network for a substance, the device configuration is automatically corrected so that the count value of the substance counter assigned to the substance falls within the proper range, and the operation of the apparatus is restarted for simulation. The operation can be continued.

  Next, a case where a multicellular biochemical reaction is simulated will be described. FIG. 5 is a schematic view for explaining a method of simulating a multicellular biochemical reaction. As shown in FIG. 5, each cell is divided into a plurality of cells CE (cells without hatching in the figure) as in FIG. 3, and the cell wall existing between the cells is divided into a plurality of cell wall cells WC (hatching in the figure). Cell). In this case, in each cell, a biochemical reaction is simulated in the same manner as the intracellular simulation described with reference to FIGS.

  In addition, the portion of the cell wall cell WC that represents the cell wall may be simulated, for example, as diffusion does not occur, that is, the substance does not diffuse between cells. Similar to the cell cell, diffusion may be simulated using a diffusion circuit.

  As described above, each cell is divided into a plurality of cells, the cell wall is divided into a plurality of cell wall cells, and the amount of change of a substance due to a biochemical reaction is simulated for each cell, and between adjacent cells in the cell. By simulating the diffusion of each substance, the biochemical reaction can be simulated in the same way for many cells. At the same time, an event that rarely occurs can be detected as a correction condition, and the apparatus configuration can be automatically corrected so that the main reaction that occurs as a result can be processed.

  The hardware simulator to which the present invention is applicable is not particularly limited to the above example, and is a hardware simulator that is configured from predetermined hardware and that simulates the amount of change in the simulation target due to the reaction between the simulation targets. If it exists, it is applicable to various fields. For example, biological simulation of brain cells and neural networks, genetic evolution and individual evolution simulation of living organisms, ecosystem simulation for migratory bird movement, transportation system simulation for moving objects, evacuation simulation, numerical fluid simulation, weather simulation, logistics simulation , Power supply simulation, city simulation for city planning, etc., economic system simulation for business transactions and stock / future transactions, management simulation, electromagnetic simulation of electrical circuits and integrated circuits, electronic level simulation of semiconductors and materials Can do.

It is a block diagram which shows the structure of the hardware simulator by one embodiment of this invention. It is a schematic diagram for demonstrating the correction method of the connection state according to the count value of a substance counter. It is a schematic diagram for demonstrating the method of simulating the biochemical reaction in a cell in consideration of the concentration gradient of each substance in a cell. It is a block diagram which shows the structure of the hardware simulator in the case of simulating the spreading | diffusion of the substance in two cells shown in FIG. It is the schematic for demonstrating the method of simulating the biochemical reaction of a multicell.

Explanation of symbols

R1 to Rn Random number generator K1 to Kn Enzyme counter V1 to Vn Restriction circuit H1 to Hn Reaction execution circuit B1 to Bm Substance counter SW Connection switching circuit CC Connection change control unit

Claims (5)

A hardware simulator configured with predetermined hardware and simulating the amount of change of the simulation object due to the reaction between the simulation objects,
A plurality of computing elements for computing values related to the simulation target;
A plurality of reaction circuits that change the value of the computing element in accordance with a reaction between the simulation objects;
A switching circuit that switches connection between the reaction circuit and the computing element in accordance with a reaction between the simulation objects;
It is determined whether or not a predetermined correction condition is satisfied based on the value of the arithmetic element, and when it is determined that the correction condition is satisfied, the operation of the apparatus is stopped and the reaction circuit and the arithmetic element A hardware simulator, comprising: a correcting unit that controls the switching circuit so as to change a connection state and corrects a connection state between the reaction circuit and the arithmetic element, and then restarts an operation of the apparatus. The computing element is provided for each group obtained by grouping a plurality of second simulation objects assigned to the first simulation object and reacting with the first simulation object. Including a plurality of counting circuits for counting values relating to the object;
The reaction circuit reduces the count value of the count circuit that represents the amount of each simulation target object before the reaction according to the progress state of the reaction, and the count value of the count circuit that represents the amount of each simulation target object after the reaction The hardware simulator according to claim 1, wherein the hardware simulator is increased.   The correction means determines whether the count value of one count circuit among the plurality of count circuits has reached a predetermined lower limit value as the correction condition, and the count value of the one count circuit is set to a lower limit value If it is determined that the number of connections has been reached, the operation of the apparatus is stopped, and the reaction circuit that increases the one count circuit and the number of connections between the one count circuit and the other count circuit are increased. 3. A correction circuit for restarting the operation of the apparatus after correcting the connection state between the reaction circuit and the count circuit by controlling the switching circuit so as to increase from the number of connections to the counter circuit. The described hardware simulator.   The correction means determines whether the count value of one count circuit among the plurality of count circuits has reached a predetermined upper limit value as the correction condition, and sets the count value of the one count circuit to an upper limit value. If it is determined that the number of connections has been reached, the operation of the apparatus is stopped, and the reaction circuit that reduces the one count circuit and the number of connections between the one count circuit and the other count circuit are reduced. 3. A correction circuit for restarting the operation of the apparatus after correcting the connection state between the reaction circuit and the count circuit by controlling the switching circuit so as to increase from the number of connections to the counter circuit. Or the hardware simulator of 3.   The hardware simulator according to claim 1, wherein the correction unit includes a host computer.

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