T. Tlusty

The Physical Logic of Protein Machines

This paper explores how the physical principles of protein machines determine their functionality and how sequences encode dynamics and interactions.

AI-predicted protein deformation encodes energy landscape perturbation

The paper uses AlphaFold2 to predict structural deformation from mutations and finds that physical strain correlates well with experimental folding free energy changes, suggesting structures encode energy landscape details.

Gene Birth in a Model of Non-genic Adaptation

This study models the conditions under which non-genic loci can become functional, finding that strict conditions are required for successful functionalization.

AlphaFold2 can predict single-mutation effects

The paper evaluates AlphaFold2's ability to predict single-mutation effects using structural and phenotypic correlations across thousands of proteins.

General theory of specific binding: insights from a genetic, mechano-chemical protein model

The paper presents a model combining chemistry, mechanics, and genetics to explain how proteins evolve high specificity through precision and size, making testable predictions about discrimination mechanisms.

de novo gene birth as an inevitable consequence of adaptive evolution

The paper hypothesizes that de novo gene birth is driven by beneficial mutations in non-genic regions and shows this mechanism aligns with genomic observations.

Spontaneous Chiral Symmetry Breaking in a Random Driven Chemical System

This paper shows that chiral symmetry breaking can occur spontaneously in a random driven chemical system by harnessing environmental energy sources.

Acceleration of enzymatic catalysis by active hydrodynamic fluctuations

The paper investigates how active hydrodynamic fluctuations influence enzymatic catalytic rates, finding that fast noise components enhance reaction rates while slow components have little effect.

Structural asymmetry along protein sequences and co-translational folding

The paper analyzes protein structures to show that structural asymmetry correlates with co-translational folding rates, proposing that evolutionary pressure favors positioning slower-folding elements near the N-terminal.

Kinetic Proofreading and the Limits of Thermodynamic Uncertainty

The paper analyzes DNA replication and translation systems using thermodynamic uncertainty relations to show how kinetic proofreading mechanisms balance precision and energy dissipation.

Green function of correlated genes and themechanical evolution of protein

The paper introduces a mechanical framework linking protein sequence, dynamics, and function through the Green function, showing how epistasis arises from nonlinearity in force propagation.