Related papers: Synchronized Pivots
Computer simulations show that liquids of molecules with harmonic intramolecular bonds may have "pseudoisomorphic" lines of approximately invariant dynamics in the thermodynamic phase diagram. We demonstrate that these lines can be…
We review and further develop an analytical model that describes how thermodynamic constraints on the stability of the native state influence protein evolution in a site-specific manner. To this end, we represent both protein sequences and…
Phase-separated biomolecular condensates exhibit a wide range of dynamical properties, which depend on the sequences of the constituent proteins and RNAs. However, it is unclear to what extent condensate dynamics can be tuned without also…
Protein function depends on both protein structure and amino acid (aa) sequence. Here we show that modular features of both structure and function can be quantified from the aa sequences alone for the small (40,42 aa) plaque-forming amyloid…
A comprehensive, semi-quantitative model for the thermodynamics of hydrophobic solvation is presented. The model is based on a very simple premise suggested by the scaled particle theory and treats both solute and solvent molecules as hard…
We develop a geometric foundation of microcanonical thermodynamics in which entropy and its derivatives are determined from the geometry of phase space, rather than being introduced through an a priori ensemble postulate. Once the minimal…
The behavior of proteins near interfaces is relevant for biological and medical purposes. Previous results in bulk show that, when the protein concentration increases, the proteins unfold and, at higher concentrations, aggregate. Here, we…
Self-propelled microparticles create flow fields that determine how they interact with surfaces, external flows, and each other. These flow fields fall into distinct classes--pushers, pullers, and neutral swimmers--each exhibiting…
Monoclonal antibody solutions are set to become a major therapeutic tool in the years to come, capable of targeting various diseases by clever designing their antigen binding site. However, the formulation of stable solutions suitable for…
We study the statistical properties of hydrophobic/polar model sequences with unique native states on the square lattice. It is shown that this ensemble of sequences differs from random sequences in significant ways in terms of both the…
Water plays a fundamental role in the structure and function of proteins and other biomolecules. The thermodynamic profile of water molecules surrounding a protein are critical for ligand binding and recognition. Therefore, identifying the…
The question of whether proteins originate from random sequences of amino acids is addressed. A statistical analysis is performed in terms of blocked and random walk values formed by binary hydrophobic assignments of the amino acids along…
Thermodynamic tools are well suited to connecting evolution of protein functionalities to mutations of amino acid sequences, especially for neuronal network structures. These tools enable one to quantify changes in modular structure and…
Phases with distinct thermodynamic properties must differ in their underlying distributions of microscopic structures. While ordered phases are readily distinguished by unit cells and space groups, the local structural basis differentiating…
The thermodynamical properties of heterogeneous DNA sequences are computed by path integral techniques applied to a nonlinear model Hamiltonian. The base pairs relative displacements are interpreted as time dependent paths whose amplitudes…
The design and optimization of antibodies requires an intricate balance across multiple properties. Protein inverse folding models, capable of generating diverse sequences folding into the same structure, are promising tools for maintaining…
Human metapneumovirus (hMPV) poses serious risks to pediatric, elderly, and immunocompromised populations. Traditional antibody discovery pipelines require 10-12 months, limiting their applicability for rapid outbreak response. This project…
The swimming trajectories of self-propelled organisms or synthetic devices in a viscous fluid can be altered by hydrodynamic interactions with nearby boundaries. We explore a multipole description of swimming bodies and provide a general…
Hydrophobic interactions are central to biological self-assembly and soft matter organization, yet their microscopic origins remain debated. A key hallmark is the strengthening of attraction between hydrophobic solutes with increasing…
PHAST is a software package written in standard Fortran, with MPI and CUDA extensions, able to efficiently perform parallel multicanonical Monte Carlo simulations of single or multiple heteropolymeric chains, as coarse-grained models for…