arXiv subjects

Dmitry V. Matyushov

Publications and source records attributed to Dmitry V. Matyushov.

At least 37 records · Page 2Linked to original sources

arXiv2011

Dissipative electro-elastic network model of protein electrostatics

We propose a dissipative electro-elastic network model (DENM) to describe the dynamics and statistics of electrostatic fluctuations at active sites of proteins. The model combines the harmonic network of residue beads with overdamped dynamics of the normal modes of the network characterized by two friction coefficients. The electrostatic component is introduced to the model through atomic charges of the protein force field. The overall effect of the electrostatic fluctuations of the network is recorded through the frequency-dependent response functions of the electrostatic potential and electric field at the active site. We also consider the dynamics of displacements of individual residues in the network and the dynamics of distances between pairs of residues. The model is tested against loss spectra of residue displacements and the electrostatic potential and electric field at the heme's iron from all-atom molecular dynamics simulations of three hydrated globular proteins.

physics.bio-ph↗

arXiv2011

Dipolar response of hydrated proteins

The paper presents an analytical theory and numerical simulations of the dipolar response of hydrated proteins. The effective dielectric constant of the solvated protein, representing the average dipole moment induced at the protein by a uniform external field, shows a remarkable variation among the proteins studied by numerical simulations. It changes from 0.5 for ubiquitin to 640 for cytochrome c. The former value implies a negative dipolar susceptibility of ubiquitin, that is a dia-electric dipolar response and negative dielectrophoresis. It means that a protein carrying an average dipole of ~240 D is expected to repel from the region of a stronger electric field. This outcome is the result of a negative cross-correlation between the protein and water dipoles, compensating for the positive variance of the protein dipole in the overall dipolar susceptibility. This phenomenon can be characterized as overscreening of protein's dipole by the hydration shell. In contrast to the neutral ubiquitin, charged proteins studied here show para-electric dipolar response and positive dielectrophoresis. The protein-water dipolar cross-correlations are long-ranged, extending approximately 2 nm from the protein surface into the bulk. The analysis of numerical simulations suggests that the polarization of the protein-water interface is strongly affected by the distribution of the protein surface charge. This component of the protein dipolar response gains in importance for high frequencies, above the protein Debye peak, when the response of the protein dipole becomes dynamically arrested. The interface response found in simulations suggests a possibility of a positive increment of the high-frequency dielectric constant of the solution compared to the dielectric constant of the solvent, in support of the observed THz absorbance of protein solutions.

physics.bio-ph↗

arXiv2011

Electric field inside a "Rossky cavity" in uniformly polarized water

Electric field produced inside a solute by a uniformly polarized liquid is strongly affected by dipolar polarization of the liquid at the interface. We show, by numerical simulations, that the electric "cavity" field inside a hydrated non-polar solute does not follow the predictions of standard Maxwell's electrostatics of dielectrics. Instead, the field inside the solute tends, with increasing solute size, to the limit predicted by the Lorentz virtual cavity. The standard paradigm fails because of its reliance on the surface charge density at the dielectric interface determined by the boundary conditions of the Maxwell dielectric. The interface of a polar liquid instead carries a preferential in-plane orientation of the surface dipoles thus producing virtually no surface charge. The resulting boundary conditions for electrostatic problems differ from the traditional recipes, affecting the microscopic and macroscopic fields based on them. We show that relatively small differences in cavity fields propagate into significant differences in the dielectric constant of an ideal mixture. The slope of the dielectric increment of the mixture versus the solute concentration depends strongly on which polarization scenario at the interface is realized. A much steeper slope found in the case of Lorentz polarization also implies a higher free energy penalty for polarizing such mixtures.

cond-mat.soft↗

arXiv2011

Potential-tuning molecular dynamics studies of fusion, and the question of ideal glassformers: (I) The Gay-Berne model

The ability of some liquids to vitrify during supercooling is usually seen as a consequence of the rates of crystal nucleation (and/or crystal growth) becoming small- thus a matter of kinetics. However there is evidence, dating back to the empirics of coal briquetting for maximum trucking efficiency, that ellipsoids pack efficiently when disordered. Noting that key studies of non-spherical object packing have never been followed from hard ellipsoids or spherocylinders (diatomics excepted) into the world of molecules with attractive forces, we have made a molecular dynamics MD study of crystal melting and glass formation on the Gay- Berne (G-B) model of ellipsoidal objects across the aspect ratio range of the hard ellipsoid studies. Here we report that, in the aspect ratio range of maximum ellipsoid packing efficiency, various G-B crystalline states, that cannot be obtained directly from the liquid, disorder spontaneously near 0 K and transform to liquids without any detectable enthalpy of fusion. Without claiming to have proved the existence of single component examples, we use the present observations, together with our knowledge of non-ideal mixing effects, to discuss the probable existence of "ideal glassformers" - single or multicomponent liquids that vitrify before ever becoming metastable with respect to crystals. The existence of crystal-free routes to the glassy state removes any precrystalline fluctuation perspective from the "glass problem". Unexpectedly we find that liquids with aspect ratios in the "crystallophobic" range also behave in an unusual (non-hysteritic) way during temperature cycling through the glass transition. We link this to the highly volume fraction-sensitive ("fragile") behavior observed in recent hard dumbbell studies at similar length/diameter ratios.

cond-mat.soft↗

arXiv2011

Non-Gaussian statistics of electrostatic fluctuations of hydration shells

We report the statistics of electric field fluctuations produced by SPC/E water inside a Kihara solute given as a hard-sphere core with a Lennard-Jones layer at its surface. The statistics of electric field fluctuations, obtained from numerical simulations, are studied as a function of the magnitude of a point dipole placed close to the solute-water interface. The free energy surface as a function of the electric field projected on the dipole direction shows a cross-over with the increasing dipole magnitude. While it is a single-well harmonic function at low dipole values, it becomes a double-well surface at intermediate dipole moment magnitudes, transforming to a single-well surface, with a non-zero minimum position, at still higher dipoles. A broad intermediate region where the interfacial waters fluctuate between the two minima is characterized by intense field fluctuations, with non-Gaussian statistics and the variance far exceeding the linear-response expectations. The excited state of the surface water is found to be lifted above the ground state by the energy required to break approximately two hydrogen bonds. This state is pulled down in energy by the external electric field of the solute dipole, making it readily accessible to thermal excitations. The excited state is a localized surface defect in the hydrogen-bond network creating a stress in the nearby network, but otherwise relatively localized in the region closest to the solute dipole.

cond-mat.soft↗

arXiv2010

Electrostatic fluctuations promote the dynamical transition in proteins

Atomic displacements of hydrated proteins are dominated by phonon vibrations at low temperatures and by dissipative large-amplitude motions at high temperatures. A crossover between the two regimes is known as a dynamical transition. Recent experiments indicate a connection between the dynamical transition and the dielectric response of the hydrated protein. We analyze two mechanisms of the coupling between the protein atomic motions and the protein-water interface. The first mechanism considers viscoelastic changes in the global shape of the protein plasticized by its coupling to the hydration shell. The second mechanism involves modulations of the motions of partial charges inside the protein by electrostatic fluctuations. The model is used to analyze mean square displacements of iron of metmyoglobin reported by Moessbauer spectroscopy. We show that high flexibility of heme iron at physiological temperatures is dominated by electrostatic fluctuations. Two onsets, one arising from the viscoelastic response and the second from electrostatic fluctuations, are seen in the temperature dependence of the mean square displacements when the corresponding relaxation times enter the instrumental resolution window.

physics.bio-ph↗

arXiv2010

Ferroelectric hydration shells around proteins: Electrostatics of the protein/water interface

Numerical simulations of hydrated proteins show that protein hydration shells are polarized into a ferroelectric cluster with a large magnitude of its average dipole moment. The emergence of this new mesophase dramatically alters the statistics of electrostatic fluctuations at the protein/water interface. The linear-response relation between the average electrostatic potential and its variance breaks down, with the breadth of the electrostatic noise far exceeding the expectations of the linear response theories. The dynamics of these non-Gaussian electrostatic fluctuations are dominated by a slow (~ 1 ns) component which freezes in at the temperature of dynamical transition of proteins.

physics.bio-ph↗

arXiv2010

Cavity-water interface is polar

We present the results of numerical simulations of the electrostatics and dynamics of water hydration shells surrounding Kihara cavities given by a Lennard-Jones (LJ) layer at the surface of a hard-sphere cavity. The local dielectric response of the hydration layer substantially exceeds that of bulk water, with the magnitude of the dielectric constant peak in the shell increasing with the growing cavity size. The polar shell propagates into bulk water to approximately the cavity radius. The statistics of the electrostatic field produced by water inside the cavity follow linear response and approach the prediction of continuum electrostatics with increasing cavity size.

physics.bio-ph↗

arXiv2008

Electrostatic fluctuations in cavities within polar liquids and thermodynamics of polar solvation

We present the results of numerical simulations of fluctuations of the electrostatic potential and electric field inside cavities created in the fluid of dipolar hard spheres. We found that the thermodynamics of polar solvation dramatically changes its regime when the cavity size becomes about 4-5 times larger than the size of the liquid particle. The range of small cavities can be reasonably understood within the framework of current solvation models. On the contrary, the regime of large cavities is characterized by a significant softening of the cavity interface resulting in a decay of the fluctuation variances with the cavity size much faster than anticipated by both the continuum electrostatics and microscopic theories. For instance, the variance of potential decays with the cavity size $R_0$ approximately as $1/R_0^{4-6}$ instead of the $1/R_0$ scaling expected from standard electrostatics. Our results suggest that cores of non-polar molecular assemblies in polar liquids lose solvation strength much faster than is traditionally anticipated.

physics.chem-ph↗

arXiv2008

Dynamical transition, hydrophobic interface, and the temperature dependence of electrostatic fluctuations in proteins

Molecular dynamics simulations have revealed a dramatic increase, with increasing temperature, of the amplitude of electrostatic fluctuations caused by water at the active site of metalloprotein plastocyanin. The increased breadth of electrostatic fluctuations, expressed in terms of the reorganization energy of changing the redox state of the protein, is related to the formation of the hydrophobic protein/water interface allowing large-amplitude collective fluctuations of the water density in the protein's first solvation shell. On the top of the monotonic increase of the reorganization energy with increasing temperature, we have observed a spike at 220 K also accompanied by a significant slowing of the exponential collective Stokes shift dynamics. In contrast to the local density fluctuations of the hydration-shell waters, these spikes might be related to the global property of the water solvent crossing the Widom line.

physics.bio-ph↗

arXiv2008

Energetics and Kinetics of Primary Charge Separation in Bacterial Photosynthesis

We report the results of Molecular Dynamics (MD) simulations and formal modeling of the free energy surfaces and reaction rates of primary charge separation in the reaction center of \textit{Rhodobacter sphaeroides}. Two simulation protocols were used to produce MD trajectories. Standard force field potentials were employed in the first protocol. In the second protocol, the special pair was made polarizable to reproduce a high polarizability of its photoexcited state observed by Stark spectroscopy. The charge distribution between covalent and charge-transfer states of the special pair was dynamically adjusted during the simulation run. We found from both protocols that the breadth of electrostatic fluctuations of the protein/water environment far exceeds previous estimates resulting in about 1.6 eV reorganization energy of electron transfer in the first protocol and 2.5 eV in the second protocol. Most of these electrostatic fluctuations become dynamically frozen on the time-scale of primary charge separation resulting in much smaller solvation contributions to the activation barrier. A non-ergodic formulation of the diffusion-reaction electron transfer kinetics has allowed us to reproduce the experimental results for both the temperature dependence of the rate and the non-exponential decay of the population of the photoexcited special pair.

physics.bio-ph↗

arXiv2007

Thermodynamics and Dynamics of a Monoatomic Glass-Former. Constant Pressure and Constant Volume Behavior

We report constant-volume and constant-pressure simulations of the thermodynamic and dynamic properties of the low-temperature liquid and crystalline phases of the modified Stillinger-Weber (mSW) model. We have found an approximately linear increase of the effective Gaussian width of the distribution of inherent structures. This effect comes from non-Gaussianity of the landscape and is consistent with the predictions of the Gaussian excitations model representing the thermodynamics of the configurational manifold as an ensemble of excitations, each carrying an excitation entropy. The mSW model provides us with both the configurational and excess entropies, with the difference mostly attributed to vibrational anharmonicity. We therefore can address the distinction between the excess thermodynamic quantities often used in the Adam-Gibbs (AG) equation. We find a new break in the slope of the constant pressure AG plot when the excess entropy is used in the AG equation. The simulation diffusivity data are equally well fitted by applying a new equation, derived within the Gaussian excitations model, that emphasizes enthalpy over entropy as the thermodynamic control variable for transport in viscous liquids.

cond-mat.soft↗

arXiv2007

Redox Entropy of Plastocyanin: Developing a Microscopic View of Mesoscopic Polar Solvation

We report applications of analytical formalisms and Molecular Dynamics (MD) simulations to the calculation of redox entropy of plastocyanin metalloprotein in aqueous solution. The goal of our analysis is to establish critical components of the theory required to describe polar solvation at the mesoscopic scale. The analytical techniques include a microscopic formalism based on structure factors of the solvent dipolar orientations and density and continuum dielectric theories. The microscopic theory employs the atomistic structure of the protein with force-field atomic charges and solvent structure factors obtained from separate MD simulations of the homogeneous solvent. The MD simulations provide linear response solvation free energies and reorganization energies of electron transfer in the temperature range 280--310 K. We found that continuum models universally underestimate solvation entropies, and a more favorable agreement is reported between the microscopic calculations and MD simulations. The analysis of simulations also suggests that difficulties of extending standard formalisms to protein solvation are related to the inhomogeneous structure of the solvation shell at the protein-water interface combining islands of highly structured water around ionized residues along with partial dewetting of hydrophobic patches. Quantitative theories of electrostatic protein hydration need to incorporate realistic density profile of water at the protein-water interface.

physics.bio-ph↗

arXiv2007

What are the benefits of bound (protonation) states for the electron-transfer kinetics?

We describe a model of electron transfer reactions affected by local binding to the donor or acceptor sites of a particle in equilibrium with the solution. The statistics of fluctuations of the donor-acceptor energy gap caused by binding/unbinding events are non-Gaussian, and the resulting free energy surfaces of electron transfer are non-parabolic. The band-width of the charge-transfer optical transition is predicted to pass through a maximum as a function of the concentration of binding particles in the solution. The model is used to rationalize recent observations of pH-dependence of electron transfer rates involving changes in the protonation state of the donor-acceptor complex.

physics.bio-ph↗

arXiv2007

Cavity Field in Molecular Liquids. When a Polar Liquid Becomes a Dielectric?

We present the results of an analytical theory and simulations of the field inside a cavity created in a dipolar liquid placed in a uniform external electric field. The analytical theory shows that the limit of continuum electrostatics is reached through a singularity in the microscopic response function responsible for a non-decaying longitudinal polarization wave. Fields in microscopic cavities are much different from macroscopic predictions, and low-polarity dielectrics are predicted to have a continuum limit distinct from the solution of Maxwell's equations. Computer Monte Carlo simulations never reach the standard continuum limit and instead converge to the new continuum solution with increasing cavity size.

cond-mat.soft↗

arXiv2007

Glassy protein dynamics and gigantic solvent reorganization energy of plastocyanin

We report the results of Molecular Dynamics simulations of electron transfer activation parameters of plastocyanin metalloprotein involved as electron carrier in natural photosynthesis. We have discovered that slow, non-ergodic conformational fluctuations of the protein, coupled to hydrating water, result in a very broad distribution of donor-acceptor energy gaps far exceeding that observed for commonly studied inorganic and organic donor-acceptor complexes. The Stokes shift is not affected by these fluctuations and can be calculated from solvation models in terms of the response of the solvent dipolar polarization. The non-ergodic character of large-amplitude protein/water mobility breaks the strong link between the Stokes shift and reorganization energy characteristic of equilibrium (ergodic) theories of electron transfer. This mechanism might be responsible for low activation barriers in natural electron transfer proteins characterized by low reaction free energy.

physics.bio-ph↗

arXiv2007

Model Energy Landscapes of Low-Temperature Fluids: Dipolar Hard Spheres

An analytical model of non-Gaussian energy landscape of low-temperature fluids is developed based on the thermodynamics of the fluid of dipolar hard spheres. The entire excitation profile of the liquid, from the high temperatures to the point of ideal-glass transition, has been obtained from the Monte Carlo simulations. The fluid of dipolar hard spheres loses stability when reaching the point of ideal-glass transition transforming via a first-order transition into a columnar liquid phase of dipolar chains locally arranged in a body-centered tetragonal order.

cond-mat.soft↗

arXiv2006

Gaussian excitations model for glass-former dynamics and thermodynamics

We describe a model for the thermodynamics and dynamics of glass-forming liquids in terms of excitations from an ideal glass state to a Gaussian manifold of configurationally excited states. The quantitative fit of this three parameter model to the experimental data on excess entropy and heat capacity shows that ``fragile'' behavior, indicated by a sharply rising excess heat capacity as the glass transition is approached from above, occurs in anticipation of a first-order transition -- usually hidden below the glass transition -- to a ``strong'' liquid state of low excess entropy. The dynamic model relates relaxation to a hierarchical sequence of excitation events each involving the probability of accumulating sufficient kinetic energy on a separate excitable unit. Super-Arrhenius behavior of the relaxation rates, and the known correlation of kinetic with thermodynamic fragility, both follow from the way the rugged landscape induces fluctuations in the partitioning of energy between vibrational and configurational manifolds. A relation is derived in which the configurational heat capacity, rather than the configurational entropy of the Adam Gibbs equation, controls the temperature dependence of the relaxation times, and this gives a comparable account of the experimental observations.

cond-mat.soft↗