Back to results
US 2026/0245652 A1Published application
Mechanistic chromatin modeling with iterative optimization, nuclear envelope interactions, and editable epigenetic composition
AssigneeAltos Labs, Inc.
InventorsErik NAVARRO, William POOLE, Simone BIANCO, Ryan SPANGLER
Life of this patent
Estimating the term…
Abstract
This disclosure relates to methods and systems for determining epigenetic states resulting from epigenetic modifying processes, particularly by use of molecules dynamics and models of epigenetic modifying processes.
Claims20
A computer-implemented method comprising:
- defining an in silico chromatin complex comprising a set of particles, wherein the particles model the in silico chromatin complex as a coarse-grained model;
- defining an initial epigenetic state based on the structure and/or composition of the chromatin complex;
- defining a set of force fields, wherein each force field independently corresponds to an interaction between at least one of the particles and at least one of:
- another one of the particles or a nuclear envelope, or the force field corresponds to an interaction between at least one of the particles and the environment surrounding the in silico chromatin complex;
- defining a model of an epigenetic modifying process comprising an interaction between the in silico chromatin complex and an external factor, wherein the external factor is capable of changing the initial epigenetic state;
- accessing molecular dynamics equations comprising the set of force fields;
- iteratively a) solving the molecular dynamics equations for the in silico chromatin complex and b) applying the model of the epigenetic modifying process;
- and
- determining the subsequent epigenetic state resulting from the epigenetic modifying process.
6 more elements
A system comprising:
- one or more data processors;
- and
- a non-transitory computer-readable storage medium comprising instructions which, when executed on the one or more data processors, cause the one or more data processors to perform the computer-implemented method including:
- defining an in silico chromatin complex comprising a set of particles, wherein the particles model the in silico chromatin complex as a coarse-grained model;
- defining an initial epigenetic state based on the structure and/or composition of the chromatin complex;
- defining a set of force fields, wherein each force field independently corresponds to an interaction between at least one of the particles and at least one of:
- another one of the particles or a nuclear envelope, or the force field corresponds to an interaction between at least one of the particles and the environment surrounding the in silico chromatin complex;
- defining a model of an epigenetic modifying process comprising an interaction between the in silico chromatin complex and an external factor, wherein the external factor is capable of changing the initial epigenetic state;
- accessing molecular dynamics equations comprising the set of force fields;
- iteratively a) solving the molecular dynamics equations for the in silico chromatin complex and b) applying the model of the epigenetic modifying process;
- and
- determining the subsequent epigenetic state resulting from the epigenetic modifying process.
9 more elements
A computer-program product tangibly embodied in a non-transitory machine-readable storage medium, comprising instructions configured to cause one or more data processors to perform the computer-implemented method including:
- defining an in silico chromatin complex comprising a set of particles, wherein the particles model the in silico chromatin complex as a coarse-grained model;
- defining an initial epigenetic state based on the structure and/or composition of the chromatin complex;
- defining a set of force fields, wherein each force field independently corresponds to an interaction between at least one of the particles and at least one of:
- another one of the particles or a nuclear envelope, or the force field corresponds to an interaction between at least one of the particles and the environment surrounding the in silico chromatin complex;
- defining a model of an epigenetic modifying process comprising an interaction between the in silico chromatin complex and an external factor, wherein the external factor is capable of changing the initial epigenetic state;
- accessing molecular dynamics equations comprising the set of force fields;
- iteratively a) solving the molecular dynamics equations for the in silico chromatin complex and b) applying the model of the epigenetic modifying process;
- and
- determining the subsequent epigenetic state resulting from the epigenetic modifying process.
6 more elements
Dependencies are inferred from the claim text.