The human genome is arranged in the cell nucleus nonrandomly, and phase separation has been proposed as an important driving force for organization. However, active system, contribution of nonequilibrium activities to structure dynamics remains be explored. We simulated using energy function parametrized with chromosome conformation capture (Hi-C) data presence active, nondirectional forces that break detailed balance. found may arise from transcription chromatin remodeling can dramatically...

The intricate structural organization of the human nucleus is fundamental to cellular function and gene regulation. Recent advancements in experimental techniques, including high-throughput sequencing microscopy, have provided valuable insights into nuclear organization. Computational modeling has played significant roles interpreting observations by reconstructing high-resolution ensembles uncovering principles. However, absence standardized tools poses challenges for furthering...

The intricate structural organization of the human nucleus is fundamental to cellular function and gene regulation. Recent advancements in experimental techniques, including high-throughput sequencing microscopy, have provided valuable insights into nuclear organization. Computational modeling has played significant roles interpreting observations by reconstructing high-resolution ensembles uncovering principles. However, absence standardized tools poses challenges for furthering...

The intricate structural organization of the human nucleus is fundamental to cellular function and gene regulation. Recent advancements in experimental techniques, including high-throughput sequencing microscopy, have provided valuable insights into nuclear organization. Computational modeling has played significant roles interpreting observations by reconstructing high-resolution ensembles uncovering principles. However, absence standardized tools poses challenges for furthering...

Some of the most potent antifreeze proteins (AFPs) are approximately rigid helical structures that bind with one side in contact ice surface at specific orientations. These AFPs take random orientations solution; however, become sterically inaccessible as AFP approaches surface. The effect these on rate adsorption to has never been explored. Here, we present a diffusion-controlled theory kinetics accounts for orientational restrictions predict constant (kon, m/s) function length and width...

Abstract The three-dimensional (3D) organization of eukaryotic genomes plays an important role in genome function. While significant progress has been made deciphering the folding mechanisms individual chromosomes, principles dynamic large-scale spatial arrangement all chromosomes inside nucleus are poorly understood. We use polymer simulations to model diploid human compartmentalization relative nuclear bodies such as lamina, nucleoli, and speckles. show that a self-organization process...

The adsorption of large rod-like molecules or crystallites on a flat crystal face, similar to Buffon's needle, requires the rods "land," with their binding sites in precise orientational alignment matching surface. An example is provided by long, helical antifreeze proteins (AFPs), which bind at specific facets and orientations ice constraint for adsorption, combination loss freedom as molecule diffuses toward surface, results an entropic barrier that hinders adsorption. Prior kinetic models...

Existing methods to compute free-energy differences between polymorphs use harmonic approximations, advanced non-Boltzmann bias sampling techniques, and/or multistage perturbations. This work demonstrates how Bennett's diabat interpolation method (J. Comput. Phys. 1976, 22, 245) can be combined with energy gaps from lattice-switch Monte Carlo techniques (Phys. Rev. E 2000, 61, 906) swiftly estimate polymorph differences. The new requires only two unbiased molecular dynamics simulations, one...

Lattice-switch Monte Carlo and the related diabat methods have emerged as efficient accurate ways to compute free energy differences between polymorphs. In this work, we introduce a one-to-one mapping from reference positions displacements in one molecular crystal another. Two features of facilitate lattice-switch for computing polymorph differences. First, is unitary so that its Jacobian does not complicate calculations. Second, easily implemented crystals arbitrary complexity. We...

Polymorph free-energy differences are critical to several applications. A recently proposed diabat interpolation framework estimated between polymorphs by quadratic of diabats. This work extends the Zwanzig-Bennett relation NPT ensemble so that diabats directly give Gibbs differences. We also demonstrate how approach can be used in cases where not parabolic. illustrate method for difference zirconium (BCC and HCP phases) compare it with conventional lattice switch Monte Carlo approach.

The intricate structural organization of the human nucleus is fundamental to cellular function and gene regulation. Recent advancements in experimental techniques, including high-throughput sequencing microscopy, have provided valuable insights into nuclear organization. Computational modeling has played significant roles interpreting observations by reconstructing high-resolution ensembles uncovering principles. However, absence standardized tools poses challenges for furthering...

Reactive crystallizations enable process streamlining by combining reaction and crystallization together in one processing step. In many cases, reactive could be equilibrium limited due to the inherent nature of participating chemical species. There is a need understand rate generation supersaturation such develop purification particle engineering strategies. The delivery burden on immense if they are part terminal Active Pharmaceutical Ingredient (API) synthesis isolation. this article, we...

For inertial reaction dynamics, a transition state theory rate constant obtained from an inaccurate coordinate can be posteriori corrected with reactive flux methods. In contrast, errors in overdamped mean first passage time calculations cannot corrected. This work develops version of the transmission coefficient. The calculation requires information committor analyses and estimate diffusivity along coordinate. We illustrate for simple two-dimensional potential that admits exact solutions.

Abstract The intricate structural organization of the human nucleus is fundamental to cellular function and gene regulation. Recent advancements in experimental techniques, including high-throughput sequencing microscopy, have provided valuable insights into nuclear organization. Computational modeling has played significant roles interpreting observations by reconstructing high-resolution ensembles uncovering principles. However, absence standardized tools poses challenges for furthering...

Abstract The human genome is arranged in the cell nucleus non-randomly, and phase separation has been proposed as an important driving force for organization. However, active system, contribution of non-equilibrium activities to structure dynamics remains be explored. We simulated using energy function parameterized with chromosome conformation capture (Hi-C) data presence active, nondirectional forces that break detailed balance. found may arise from transcription chromatin remodeling can...