protein folding

RojhanGenomics/tp53-prima1-md-simulation: v2.0.0 - Post-review revision: topology fix, additional analyses (IE, decomposition, DSSP, Zn), negative control, 4th replicate, cross-engine docking validation

[Post-submission revision] - 2026-09 Following a desk rejection from JBSD (concerns: depth of analysis, novelty, rationale clarity), the following additional analyses and fixes were made. Fixed Protein topology (Leu289 truncation): topology/topol_Protein_chain_A.itp was found to be missing 11 atoms (CD1/CD2 side chain...

Laser preconditioning with a 755-nm picosecond diffractive lens array accelerates cutaneous wound healing via early activation of reparative gene networks

Preconditioning the skin with non-ablative laser energy represents a promising strategy to enhance tissue repair, yet its biological mechanisms remain incompletely defined. This study investigated whether pre-injury stimulation using a 755-nm picosecond Alexandrite laser (PSAL) equipped with a diffractive lens array (D...

RojhanGenomics/tp53-prima1-md-simulation: v2.0.0 - Post-review revision: topology fix, additional analyses (IE, decomposition, DSSP, Zn), negative control, 4th replicate, cross-engine docking validation

[Post-submission revision] - 2026-09 Following a desk rejection from JBSD (concerns: depth of analysis, novelty, rationale clarity), the following additional analyses and fixes were made. Fixed Protein topology (Leu289 truncation): topology/topol_Protein_chain_A.itp was found to be missing 11 atoms (CD1/CD2 side chain...

Computational Exploration of the Structural, Electronic and Nonlinear Optical Properties of Substituted Piperidine Scaffold: A DFT and Molecular Docking Approach

An investigation into the structural, electronic and reactive properties of a substituted piperidine scaffold were conducted using density functional theory (DFT) at the B3LYP/6-31 G(d) level of theory. Molecular geometry optimization established a stable equilibrium structure. Frontier molecular orbital (FMO) analysis...

ESMCHalo: homology-aware halophile-associated protein prediction with leakage-free knowledge distillation

ESMCHalo is a frozen protein-sequence predictor that combines ESMC-600M layer-36 canonical mean representations with five compact student heads trained using leakage-free out-of-fold knowledge distillation. The release provides frozen inference code, model checkpoints, calibration, a fixed threshold, verification utili...

Title: Phase Transition Modeling with Emergent Control

This paper presents a novel approach to modeling phase transitions, specifically focusing on the emergence of control within complex systems. We introduce a dynamic resonance field that evolves in response to the system's state, generating feedback loops that influence the transition process. This mechanism allows for...

Thermodynamic Profiling for Synonymous Variant Classification: When the Message Changes Without Changing the Protein

In synonymous variants, the signal of pathogenicity is detectable as a local, signed thermodynamic perturbation of nearest-neighbor nucleotide stacking — orthogonal to protein-level predictors — that a two-feature interpretable model reproduces at the level of a dedicated deep classifier, and whose clarity increases wi...

Molecular identification and statistical optimization of endo-α-amylase production by Bacillus licheniformis KeR9 isolated from potato roots for maltooligosaccharide synthesis

A starch-degrading bacterial strain (KeR9) isolated from potato root tissues was identified through whole-genome sequencing using average nucleotide identity (ANI) and DNA-DNA hybridization (DDH) as Bacillus licheniformis . This strain with enzymatic production potential was then deposited in the Genbank project PRJNA1...

Title: Phase Transition Modeling with Emergent Control

This paper presents a novel approach to modeling phase transitions, specifically focusing on the emergence of control within complex systems. We introduce a dynamic resonance field that evolves in response to the system's state, generating feedback loops that influence the transition process. This mechanism allows for...

Thermodynamic Profiling for Synonymous Variant Classification: When the Message Changes Without Changing the Protein

In synonymous variants, the signal of pathogenicity is detectable as a local, signed thermodynamic perturbation of nearest-neighbor nucleotide stacking — orthogonal to protein-level predictors — that a two-feature interpretable model reproduces at the level of a dedicated deep classifier, and whose clarity increases wi...

Title: Dynamical Topology Optimization for Complexity

Dynamical Topology Optimization (DTO) provides a framework for optimizing complex network topologies by iteratively refining connections based on emergent properties. This paper introduces a novel algorithm, termed 'Adaptive Topology Evolution', which integrates reinforcement learning and graph theory to achieve automa...

The evolutionarily conserved C-terminal domain of a domesticated transposase-derived protein regulates its DNA integration ability