APPARATUS FOR COMPUTING A MANY-BODY PROBLEM

• US 20080201121A1
• Filed: 02/19/2008
• Published: 08/21/2008
• Est. Priority Date: 02/20/2007
• Status: Abandoned Application

• Current Assignee: NEC Corporation
• Original Assignee: NEC Corporation
• Inventors: YANO, YUICHI
• Application Number:
  US12/033,201
• Publication Number:
  US 20080201121A1
• Time in Patent Office: Days
• US Class Current: 703/2
• CPC Class Codes: G16C 10/00 Computational theoretical chemistry, i.e. ICT specially adapted for theoretical aspects of quantum chemistry, molecular mechanics, molecular dynamics or the like

Abstract

A many-body problem computing apparatus includes a coordinate storage unit for storing coordinates of the centers of gravity of residues which particles belong to, a gravity center distance computing unit for computing a distance between the coordinates of the center of gravity of a residue which a specific particle belongs to and the coordinates of the center of gravity of a residue which the other particles belong to, and a distance comparison unit for comparing the distance computed by the distance computing unit with a cut-off distance and giving instructions to compute a force or potential if the distance is less than the cut-off distance.

Claims

1. A method of computing a many-body problem comprising a step of computing a force or potential acting on a specific particle in a system consisting of plural particles, wherein the step of computing the force or potential is conducted only on a particle pair of a residue the center of gravity of which is located at a coordinate distance less than a cut-off distance.

2. The method according to claim 1, wherein the residue is an amino acid forming a protein.

3. The method according to claim 1, further comprising a step of using a coordinate storage device, the coordinate storage device comprising:

a first coordinate storage portion for storing the coordinates (x, y, z) of the particles in the system;

a second coordinate storage portion for storing the coordinates (Rxi, Ryi, Rzi) of the centers of gravity of residues which the particles in the system belong to;

a third coordinate storage portion for storing the coordinates of a specific particle, or an i-particle; and

a fourth coordinate storage portion for storing the coordinates of the center of gravity of the residue which the i-particle belongs to,

wherein the step of using the coordinate storage device comprises;

computing an inter-particle distance based on the coordinates of the j-particle and the coordinates of the i-particle in the third coordinate storage portion,

computing a distance between the centers of gravity of the residues based on the coordinates of the j-particle and the coordinates of the center of gravity of the i-particle in the third coordinate storage portion to be compared with the cut-off distance;

making zero the computation result of the inter-particle distance when the distance between the coordinates of the centers of gravity is greater than the cut-off distance; and

computing a force or potential is computed based on the inter-particle distance obtained as the result of computation when the distance between the coordinates of the centers of gravity is smaller than the cut-off value.

4. The method according to claim 3, further comprising:

designating a first and second addresses for designating the respective addresses of the first storage portion and the second storage portion ; and

selecting an address according to the designation of the first and second addresses, wherein the selecting the address includes;

when a particle write signal is activated from an external device,

reading out the coordinates of the specific particle, or the i-particle selected by the designation of the second address from the first coordinate storage portion writing the same in the third coordinate storage portion, and

reading out the coordinates of the center of gravity of the residue which the i-particle belongs to from the second coordinate storage portion and writing the same in the fourth coordinate storage portion ; and

when the particle write signal is inactivated from the external device,

selecting an initial address of the j-particle to be computed with the i-particle set by the designation of the first address,

reading out the coordinates of the j-particle from the first coordinate storage portion and output for the distance computation,

reading out the coordinates of the center of gravity of the residue which the j-particle belongs to from the second coordinate storage portion, and

outputting for the computation of the gravity center distance, and wherein the designating of the first address includes;

incrementing the address by one on each clock pulse, whereby the computation is sequentially conducted on the j-particles, and upon completion of the computation for all the j-particles in the system;

setting the initial j-particle address; and

incrementing the designation of the second address by one so that sequential computation is conducted on the next i-particle.

5. An apparatus for computing a many-body problem comprising:

coordinate storage means for storing coordinates of the centers of gravity of residues which particles belong to;

gravity center distance computing means for computing a distance between the coordinates of the center of gravity of a residue which a specific particle belongs to and the coordinates of the center of gravity of a residue which other particles belong to; and

distance comparison means for comparing the distance obtained by the gravity center distance computing means with a cut-off distance and giving instructions to compute a force or potential if the distance is less than the cut-off distance.

6. The apparatus according to claim 5, wherein the residue is an amino acid forming a protein.

7. The apparatus according to claim 5, further comprising:

first coordinate storage means for storing the coordinates of the particles in the system;

second coordinate storage means for storing the coordinates of the centers of gravity of residues which the particles in the system belong to;

third coordinate storage means for storing the coordinates of a specific particle, or an i-particle;

fourth coordinate storage means for storing the coordinates of the center of gravity of the residue which the i-particle belongs to;

first distance computing means for computing an inter-particle distance;

second distance computing means for computing a distance between the centers of gravity of the residues;

distance comparison means for comparing the cut-off distance; and

computing means for computing a force or potential based on the inter-particle distance computed by the first distance computing means, wherein;

the coordinate storage means is used as second storage means, while the gravity center distance computing means is used as second distance computing means;

the first coordinate storage means sequentially storing the coordinates (x, y, z) of the particles in the system;

the second coordinate storage means storing the coordinates of the centers of gravity (Rx, Ry, Rz) of the residues which the particles belong to in the same sequence as the first coordinate storage means;

the coordinates (xi, yi, zi) of a specific particle, or an i-particle being read out from the first coordinate storage means and written in the third storage means, while the coordinates of the center of gravity (Rxi, Ryi, Rzi) of the residue which the i-particle belongs to are read out from the second coordinate storage means and written in the fourth coordinate storage means;

the second distance computing means computing a distance from the coordinates of the center of gravity of the residue which the i-particle belongs to stored in the fourth coordinate storage means based on the coordinates of the center of gravity of the residue which the j-particle belongs to;

the coordinates of the j-particle being used by the first distance computing means to compute a distance from the coordinates of the i-particle stored in the third coordinate storage means;

the distance comparison means comparing the distance between the coordinates of the centers of gravity with the cut-off distance, and outputting a signal to set the output of the computing means to zero when the distance is greater than the cut-off distance, and activating the output of the computing means to compute a force or potential based on the inter-particle distance computed by the first distance computing means when the distance is smaller than the cut-off distance.

8. The apparatus according to claim 7, further comprising:

first and second addressing means for designating respective addresses of the first and second coordinate storage means; and

address selection means for selecting an address of the first and second addressing means, wherein;

when a particle write signal from an external device is activated, the address selection means reads out the coordinates (xi, yi, zi) of a specific particle, or an i-particle selected by the second addressing means from the first coordinate storage means and writes the same in the third storage means, while reads out the coordinates of the center of gravity (Rxi, Ryi, Rzi) of the residue which the i-particle belongs to from the second coordinate storage means and writes the same in the fourth coordinate storage means;

when the particle write signal from the external device is inactivated, the address selection means selects the initial address of the j-particle to be computed with the i-particle set in the first address selection means, and reads out the coordinates of the j-particle from the first coordinate storage means to output the same to the first distance computing means, while reads out the coordinates of the center of gravity of the residue which the j-particle belongs to from the second coordinate storage means to output the same to the second distance computing means;

the first addressing means increments its address by one on each clock pulse to sequentially conduct computations for the j-particles and, upon completing the computations for all the j-particles in the system, sets the initial j-particle address in the first addressing means; and

the second addressing means increments its address by one to sequentially conduct computations for the next i-particle.

9. The apparatus according to claim 8, wherein the first coordinate storage means and the second coordinate storage means are connected to the address selection means in parallel to each other.

10. The apparatus according to claim 8, wherein the first coordinate storage means and the second coordinate storage means are connected to the address selection means in series.