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Boris Fain

Publications and source records attributed to Boris Fain.

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Neural Network Perturbation Theory (NNPT): Learning Residual Corrections from Exact Solutions

Many complex physical systems naturally decompose into an exactly solvable component augmented by a perturbative correction. Rather than directly employing neural networks to analyze complex physical systems, we introduce Neural Network Perturbation Theory (NNPT)--a correction learning approach that predicts residual perturbations after analytically subtracting known exact solutions. Using the gravitational three-body problem as testbed, we vary Jovian mass from f=0.05 to 30 times its physical value while holding network architecture fixed. An equalized-accuracy protocol with 1% tolerance reveals an unexpected non-monotonic capacity profile: capacity peaks at f=5 in the late integrable regime (3x32, 2242 parameters), remains elevated through the transition region (f~15-17), then decreases in the fully chaotic regime (f>=17, requiring only 2x32 with 1186 parameters)--a 47% reduction from peak. With symplectic integrator energy conservation below 2x10^{-4}, this counterintuitive phenomenon reflects genuine physical structure rather than numerical artifacts. Sequential correction experiments show negligible refinement (||y2||/||y1||~0.997), confirming single-stage networks capture dominant perturbative features without hierarchical decomposition. The capacity transition at f_c=16.6+-2.8 aligns with Chirikov's resonance-overlap criterion. Intermediate-complexity regimes impose maximal capacity requirements, while fully chaotic dynamics undergo ergodic smoothing--trajectory-specific fluctuations become irreducible noise, leaving only statistically smooth corrections requiring fewer parameters.

physics.comp-ph

A Novel Method for Sampling Alpha-Helical Protein Backbones

We present a novel technique of sampling the configurations of helical proteins. Assuming knowledge of native secondary structure, we employ assembly rules gathered from a database of existing structures to enumerate the geometrically possible three-dimensional arrangements of the constituent helices. We produce a library of possible folds for twenty-five helical protein cores. In each case, our method finds significant numbers of conformations close to the native structure. In addition we assign coordinates to all atoms for four of the twenty-five proteins and show that this has a small effect on the number of near-native conformations. In the context of database driven exhaustive enumeration our method performs extremely well, yielding significant percentages of structures (between 0.02% and 82%) within 6 Angstroms of the native structure. The method's speed and efficiency make it a valuable tool for predicting protein structure.

cond-mat.soft

Conformations of closed DNA

We examine the conformations of a model for a short segment of closed DNA. The molecule is represented as a cylindrically symmetric elastic rod with a constraint corresponding to a specification of the linking number. We obtain analytic expressions leading to the spatial configuration of a family of solutions representing distortions that interpolate between the circular form of DNA and a figure-eight form that represents the onset of interwinding. We are also able to generate knotted loops. We suggest ways to use our approach to produce other configurations relevant to studies of DNA structure. The stability of the distorted configurations is assessed, along with the effects of fluctuations on the free energy of the various configurations.

cond-mat.soft

Conformations of Circular DNA

We examine the elastic model of short circular DNA. We obtain analytic expressions for configurations, elastic energy, twist and linking number of our solutions. We find the onset of the plectonemic transition. We suggest ways to use our formalism to describe other elastic models, and to improve the current finite-element-analysis methods. We estimate the effect of thermodynamic fluctuations.

cond-mat.soft

Conformations of Linear DNA

We examine the conformations of a model for under- and overwound DNA. The molecule is represented as a cylindrically symmetric elastic string subjected to a stretching force and to constraints corresponding to a specification of the link number. We derive a fundamental relation between the Euler angles that describe the curve and the topological linking number. Analytical expressions for the spatial configurations of the molecule in the infinite- length limit were obtained. A unique configuraion minimizes the energy for a given set of physical conditions. An elastic model incorporating thermal fluctuations provides excellent agreement with experimental results on the plectonemic transition.

cond-mat.soft