Results 21 to 30 of about 1,381,598 (313)
Entropy, 2022 The underlying mechanism determining the size of a particular cell is one of the fundamental unknowns in cell biology. Here, using a new approach that could be used for most of unicellular species, we show that the protein synthesis and cell size are ...
Mohammad Razavi +2 more
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Resolving coupled pH titrations using alchemical free energy calculations
, 2023 In a protein, nearby titratable sites can be coupled: the (de)protonation of one may affect the other. The degree of this interaction depends on several factors and can influence the measured pKa. Here, we derive a formalism based on double free energy
Vytautas, Gapsys +2 more
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Entropy Pair Functional Theory: Direct Entropy Evaluation Spanning Phase Transitions
Entropy, 2021 We prove that, within the class of pair potential Hamiltonians, the excess entropy is a universal, temperature-independent functional of the density and pair correlation function. This result extends Henderson’s theorem, which states that the free energy
Donald M. Nicholson +4 more
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Synthese, 2007 If one formulates Helmholtz's ideas about perception in terms of modern-day theories one arrives at a model of perceptual inference and learning that can explain a remarkable range of neurobiological facts. Using constructs from statistical physics it can be shown that the problems of inferring what cause our sensory input and learning causal ...
Karl J. Friston, Klaas E. Stephan
openaire +3 more sources
An Open-Source Molecular Builder and Free Energy Preparation Workflow
, 2022 Automated free energy calculations for the prediction of binding free energies of congeneric series of ligands to a protein target are growing in popularity, but building reliable initial binding poses for the ligands is challenging.
Mateusz, Bieniek +5 more
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Structural Dynamics, 2019 Theoretical and experimental methodologies that can characterize electronic and nuclear dynamics, and the coupling between the two, are needed to understand photoinduced charge transfer in molecular building blocks used in organic photovoltaics.
Khadijeh Khalili +5 more
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Thermodynamic Integration in 3n Dimensions Without Biases or Alchemy for Protein Interactions
Frontiers in Physics, 2020 Thermodynamic integration (TI), a powerful formalism for computing Gibbs free energy, has been implemented for many biophysical processes with alchemical schemes that require delicate human efforts to choose/design biasing potentials for sampling the ...
Liao Y. Chen
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Attention, Uncertainty, and Free-Energy [PDF]
Frontiers in Human Neuroscience, 2010 We suggested recently that attention can be understood as inferring the level of uncertainty or precision during hierarchical perception. In this paper, we try to substantiate this claim using neuronal simulations of directed spatial attention and biased competition. These simulations assume that neuronal activity encodes a probabilistic representation
Feldman, Harriet, Friston, Karl J.
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Free Energy Profile Decomposition Analysis for QM/MM Simulations of Enzymatic Reactions
, 2023 In enzyme mechanistic studies and mutant design, it is highly desirable to know the individual residue contributions to the reaction free energy barrier.
Richard , Van +5 more
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Free-energy calculations [PDF]
, 2002 The techniques that can be used to study phase diagrams numerically depend on the character of the phase transitions. In particular, there is quite a difference among the tools used to study first-order phase transitions and those applied to analyze critical phenomena near continuous phase transitions.
Daan Frenkel, Berend Smit
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