Data processing: structural design – modeling – simulation – and em – Simulating nonelectrical device or system – Biological or biochemical
Reexamination Certificate
2011-03-15
2011-03-15
Borin, Michael (Department: 1631)
Data processing: structural design, modeling, simulation, and em
Simulating nonelectrical device or system
Biological or biochemical
Reexamination Certificate
active
07908129
ABSTRACT:
A method of simulating behaviour of a molecular system with m degrees of freedom over time comprising a partial momentum refreshment step and a molecular dynamics step, wherein the partial momentum refreshment step comprises: given a starting position q and a starting momentum p of the molecular system, partially refreshing the momentum to define refreshed momentum p′ evaluating the shadow Hamiltonian331Δtat position q and momentum p′; and accepting or rejecting the refreshed momentum p′ according to a Metropolis-type function and if p′ is accepted using p′ as the resulting momentum p and starting position q as the resulting position q or if it is rejected, using p as the resulting momentum p and starting position q as the resulting position; and wherein the molecular dynamics step comprises: given a starting position q and starting momentum p of the molecular system, running a molecular dynamics simulation over a fixed number of iterations and obtaining new position q′ and new momentum p′; evaluating the shadow Hamiltonian332Δtat position q′ and momentum p′ after the molecular dynamics simulation; and accepting or rejecting the new system configuration produced by the molecular dynamics simulation according to a Metropolis-type function and, if the new system configuration is accepted, using q′ as the resulting position q and p′ as the resulting momentum p or, if it is rejected, using the original starting position q as the resulting position q and negating the original starting momentum p to give the resulting momentum p; wherein either the partial momentum refreshment or the molecular dynamics step is the first step of the method, and the resulting position and resulting momentum of the first step provides the starting position q and starting momentum p for the next step.
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Akhmatskaya Elena Vitalievna
Nobes Ross Howard
Reich Sebastian
Borin Michael
Fujitsu Limited
Staas & Halsey , LLP
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