Meeting Doug Henderson

Eisenberg, Robert S.

doi:10.1016/j.molliq.2022.119574

Cited by 3 publications

(2 citation statements)

References 53 publications

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“…These issues are well recognized in the specialist literature of granular flow [173][174][175] but their remedy is unclear, not yet at hand [176,181,182], as far as I can tell. It is obvious that similar issues can arise when molecules pack together particularly at the very high number densities important in enzymes [183] and ion channels [184][185][186].…”

Section: Discussionmentioning

confidence: 99%

“…Ion channels are all interfaces-if one can be forgiven some vivid language-so the effect of finite size and crowding of ions in channels has become a central issue [257,258] since it was first introduced [184,247,259] and used with Monte Carlo techniques [185,260] to explain and design the selectivity of calcium and sodium channels [261][262][263][264][265]. Recent field theories include several treatments of finite size [54].…”

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confidence: 99%

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Setting Boundaries for Statistical Mechanics

Eisenberg

2022

Molecules

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Statistical mechanics has grown without bounds in space. Statistical mechanics of noninteracting point particles in an unbounded perfect gas is widely used to describe liquids like concentrated salt solutions of life and electrochemical technology, including batteries. Liquids are filled with interacting molecules. A perfect gas is a poor model of a liquid. Statistical mechanics without spatial bounds is impossible as well as imperfect, if molecules interact as charged particles, as nearly all atoms do. The behavior of charged particles is not defined until boundary structures and values are defined because charges are governed by Maxwell’s partial differential equations. Partial differential equations require boundary structures and conditions. Boundary conditions cannot be defined uniquely ‘at infinity’ because the limiting process that defines ‘infinity’ includes such a wide variety of structures and behaviors, from elongated ellipses to circles, from light waves that never decay, to dipolar fields that decay steeply, to Coulomb fields that hardly decay at all. Boundaries and boundary conditions needed to describe matter are not prominent in classical statistical mechanics. Statistical mechanics of bounded systems is described in the EnVarA system of variational mechanics developed by Chun Liu, more than anyone else. EnVarA treatment does not yet include Maxwell equations.

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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

Setting Boundaries for Statistical Mechanics

Eisenberg

2022

Molecules

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Calcium versus potassium selectivity in a nanopore: The effect of charge inversion at localized pore charges

Fábián¹,

Sarkadi²,

Valiskó³

et al. 2022

Journal of Molecular Liquids

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H-Bonds in Crambin: Coherence in an α-Helix

Minh

Eisenberg

2023

ACS Omega

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We applied coherence analysis�used by engineers to identify linear interactions in stochastic systems�to molecular dynamics simulations of crambin, a thionin storage protein found in Abyssinian cabbage. A key advantage of coherence over other analyses is that it is robust, independent of the properties, or even the existence of probability distributions often relied on in statistical mechanics. For frequencies between 0.391 and 5.08 GHz (corresponding reciprocally to times of 2.56 and 0.197 ns), the displacements of oxygen and nitrogen atoms across α-helix H-bonds are strongly correlated, with a coherence greater than 0.9; the secondary structure causes the Hbonds to effectively act as a spring. Similar coherence behavior is observed for covalent bonds and other noncovalent interactions including H-bonds in β-sheets and salt bridges. In contrast, arbitrary pairs of atoms that are physically distant have uncorrelated motions and negligible coherence. These results suggest that coherence may be used to objectively identify atomic interactions without subjective thresholds such as H-bond lengths angles and angles. Strong coherence is also observed between the average position of adjacent leaves (groups of atoms) in an α-helix, suggesting that the harmonic analysis of classical molecular dynamics can successfully describe the propagation of allosteric interactions through the structure.

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Meeting Doug Henderson

Cited by 3 publications

References 53 publications

Setting Boundaries for Statistical Mechanics

Setting Boundaries for Statistical Mechanics

Calcium versus potassium selectivity in a nanopore: The effect of charge inversion at localized pore charges

H-Bonds in Crambin: Coherence in an α-Helix

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