bcp banner
  • Volume/Page
  • Keyword
  • DOI
  • Citation
  • Advanced
   
 
 
 

Flickr Twitter iResearch App Facebook

Search Issue | RSS Feeds RSS
Previous Issue

May 2013

Volume 7, Issue 5

back to top
RSS Feeds
FREE

Perspective: Stochastic algorithms for chemical kinetics

Daniel T. Gillespie, Andreas Hellander, and Linda R. Petzold

J. Chem. Phys. 138, 170901 (2013); http://dx.doi.org/10.1063/1.4801941 (14 pages)

Online Publication Date: 1 May 2013

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We outline our perspective on stochastic chemical kinetics, paying particular attention to numerical simulation algorithms. We first focus on dilute, well-mixed systems, whose description using ordinary differential equations has served as the basis for traditional chemical kinetics for the past 150 years. For such systems, we review the physical and mathematical rationale for a discrete-stochastic approach, and for the approximations that need to be made in order to regain the traditional continuous-deterministic description. We next take note of some of the more promising strategies for dealing stochastically with stiff systems, rare events, and sensitivity analysis. Finally, we review some recent efforts to adapt and extend the discrete-stochastic approach to systems that are not well-mixed. In that currently developing area, we focus mainly on the strategy of subdividing the system into well-mixed subvolumes, and then simulating diffusional transfers of reactant molecules between adjacent subvolumes together with chemical reactions inside the subvolumes.
Show PACS
82.20.Uv Stochastic theories of rate constants
82.20.Wt Computational modeling; simulation
82.40.Bj Oscillations, chaos, and bifurcations
02.50.Ey Stochastic processes
02.60.Lj Ordinary and partial differential equations; boundary value problems
back to top
RSS Feeds

Robust and efficient configurational molecular sampling via Langevin dynamics

Benedict Leimkuhler and Charles Matthews

J. Chem. Phys. 138, 174102 (2013); http://dx.doi.org/10.1063/1.4802990 (12 pages)

Online Publication Date: 1 May 2013

Full Text: Read Online (HTML) | Download PDF

Show Abstract
A wide variety of numerical methods are evaluated and compared for solving the stochastic differential equations encountered in molecular dynamics. The methods are based on the application of deterministic impulses, drifts, and Brownian motions in some combination. The Baker-Campbell-Hausdorff expansion is used to study sampling accuracy following recent work by the authors, which allows determination of the stepsize-dependent bias in configurational averaging. For harmonic oscillators, configurational averaging is exact for certain schemes, which may result in improved performance in the modelling of biomolecules where bond stretches play a prominent role. For general systems, an optimal method can be identified that has very low bias compared to alternatives. In simulations of the alanine dipeptide reported here (both solvated and unsolvated), higher accuracy is obtained without loss of computational efficiency, while allowing large timestep, and with no impairment of the conformational exploration rate (the effective diffusion rate observed in simulation). The optimal scheme is a uniformly better performing algorithm for molecular sampling, with overall efficiency improvements of 25% or more in practical timestep size achievable in vacuum, and with reductions in the error of configurational averages of a factor of ten or more attainable in solvated simulations at large timestep.
Show PACS
87.15.ap Molecular dynamics simulation
36.20.Hb Configuration (bonds, dimensions)
31.50.-x Potential energy surfaces
87.10.Ed Ordinary differential equations (ODE), partial differential equations (PDE), integrodifferential models
87.10.Mn Stochastic modeling

Hierarchical Nyström methods for constructing Markov state models for conformational dynamics

Yuan Yao, Raymond Z. Cui, Gregory R. Bowman, Daniel-Adriano Silva, Jian Sun, and Xuhui Huang

J. Chem. Phys. 138, 174106 (2013); http://dx.doi.org/10.1063/1.4802007 (10 pages)

Online Publication Date: 2 May 2013

Full Text: Read Online (HTML) | Download PDF

Show Abstract
Markov state models (MSMs) have become a popular approach for investigating the conformational dynamics of proteins and other biomolecules. MSMs are typically built from numerous molecular dynamics simulations by dividing the sampled configurations into a large number of microstates based on geometric criteria. The resulting microstate model can then be coarse-grained into a more understandable macrostate model by lumping together rapidly mixing microstates into larger, metastable aggregates. However, finite sampling often results in the creation of many poorly sampled microstates. During coarse-graining, these states are mistakenly identified as being kinetically important because transitions to/from them appear to be slow. In this paper, we propose a formalism based on an algebraic principle for matrix approximation, i.e., the Nyström method, to deal with such poorly sampled microstates. Our scheme builds a hierarchy of microstates from high to low populations and progressively applies spectral clustering on sets of microstates within each level of the hierarchy. It helps spectral clustering identify metastable aggregates with highly populated microstates rather than being distracted by lowly populated states. We demonstrate the ability of this algorithm to discover the major metastable states on two model systems, the alanine dipeptide and trpzip2 peptide.
Show PACS
87.15.hp Conformational changes
87.15.nr Aggregation
02.50.Ga Markov processes
87.14.ef Peptides
87.15.ap Molecular dynamics simulation
87.15.bk Structure of aggregates

A simplified representation of anisotropic charge distributions within proteins

Travis Hoppe

J. Chem. Phys. 138, 174110 (2013); http://dx.doi.org/10.1063/1.4803099 (11 pages)

Online Publication Date: 3 May 2013

Full Text: Read Online (HTML) | Download PDF

Show Abstract
Effective coarse-grained representations of protein-protein interaction potentials are vital in the modeling of large scale systems. We develop a method to fit an arbitrary number of effective charges to approximate the electrostatic potential of a protein at a given pH in an ionic solution. We find that the effective charges can reproduce an input potential calculated from a high resolution Poisson-Boltzmann calculation. Since the effective charges used in this model are not constrained to the locations of the original charged groups, the extra degrees of freedom allows us to reproduce the field anisotropy with fewer charges. The fitting procedure uses a number of approximations in the charge magnitudes, initial conditions, and multipoles to speed convergence. The most significant gains are found by fitting the multipole moments of the effective charge potential to the moments of the original field. We show that the Yukawa potential is not only sufficient as a pairwise summation in reproducing the potential, but comes naturally from the linearized expansion of the Poisson-Boltzmann equation. We compute interaction energies and find excellent agreement to the original potential. From the effective charge model we compute the electrostatic contribution to the second virial coefficient.
Show PACS
87.18.Xr Proteomics

Probability of double-strand breaks in genome-sized DNA by γ-ray decreases markedly as the DNA concentration increases

Shunsuke F. Shimobayashi, Takafumi Iwaki, Toshiaki Mori, and Kenichi Yoshikawa

J. Chem. Phys. 138, 174907 (2013); http://dx.doi.org/10.1063/1.4802993 (5 pages)

Online Publication Date: 6 May 2013

Full Text: Read Online (HTML) | Download PDF

Show Abstract
By use of the single-molecule observation, we count the number of DNA double-strand breaks caused by γ-ray irradiation with genome-sized DNA molecules (166 kbp). We find that P1, the number of double-strand breaks (DSBs) per base pair per unit Gy, is nearly inversely proportional to the DNA concentration above a certain threshold DNA concentration. The inverse relationship implies that the total number of DSBs remains essentially constant. We give a theoretical interpretation of our experimental results in terms of attack of reactive species upon DNA molecules, indicating the significance of the characteristics of genome-sized giant DNA as semiflexible polymers for the efficiency of DSBs.
Show PACS
87.53.-j Effects of ionizing radiation on biological systems
87.14.gk DNA
87.18.Wd Genomics
02.50.Cw Probability theory
87.15.-v Biomolecules: structure and physical properties

On the role of thermal backbone fluctuations in myoglobin ligand gate dynamics

Andrey Krokhotin, Antti J. Niemi, and Xubiao Peng

J. Chem. Phys. 138, 175101 (2013); http://dx.doi.org/10.1063/1.4801330 (26 pages)

Online Publication Date: 6 May 2013

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We construct an energy function that describes the crystallographic structure of sperm whale myoglobin backbone. As a model in our construction, we use the Protein Data Bank entry 1ABS that has been measured at liquid helium temperature. Consequently, the thermal B-factor fluctuations are very small, which is an advantage in our construction. The energy function that we utilize resembles that of the discrete nonlinear Schrödinger equation. Likewise, ours supports topological solitons as local minimum energy configurations. We describe the 1ABS backbone in terms of topological solitons with a precision that deviates from 1ABS by an average root-mean-square distance, which is less than the experimentally observed Debye-Waller B-factor fluctuation distance. We then subject the topological multi-soliton solution to extensive numerical heating and cooling experiments, over a very wide range of temperatures. We concentrate in particular to temperatures above 300 K and below the Θ-point unfolding temperature, which is around 348 K. We confirm that the behavior of the topological multi-soliton is fully consistent with Anfinsen's thermodynamic principle, up to very high temperatures. We observe that the structure responds to an increase of temperature consistently in a very similar manner. This enables us to characterize the onset of thermally induced conformational changes in terms of three distinct backbone ligand gates. One of the gates is made of the helix F and the helix E. The two other gates are chosen similarly, when open they provide a direct access route for a ligand to reach the heme. We find that out of the three gates we investigate, the one which is formed by helices B and G is the most sensitive to thermally induced conformational changes. Our approach provides a novel perspective to the important problem of ligand entry and exit.
Show PACS
87.15.H- Dynamics of biomolecules
36.20.Ey Conformation (statistics and dynamics)
36.20.Hb Configuration (bonds, dimensions)
87.15.Cc Folding: thermodynamics, statistical mechanics, models, and pathways
87.14.E- Proteins
87.15.B- Structure of biomolecules

Non-Markovianity during the quantum Zeno effect

A. Thilagam

J. Chem. Phys. 138, 175102 (2013); http://dx.doi.org/10.1063/1.4802785 (11 pages)

Online Publication Date: 7 May 2013

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We examine the Zeno and anti-Zeno effects in the context of non-Markovian dynamics in entangled spin-boson systems in contact with noninteracting reservoirs. We identify enhanced non-Markovian signatures in specific two-qubit partitions of a Bell-like initial state, with results showing that the intra-qubit Zeno effect or anti-Zeno effect occurs in conjunction with inter-qubit non-Markovian dynamics for a range of system parameters. The time domain of effective Zeno or anti-Zeno dynamics is about the same order of magnitude as the non-Markovian time scale of the reservoir correlation dynamics, and changes in decay rate due to the Zeno mechanism appears coordinated with information flow between specific two-qubit partitions. We extend our analysis to examine the Zeno mechanism-non-Markovianity link using the tripartite states arising from a donor-acceptor-sink model of photosynthetic biosystems.
Show PACS
03.65.Xp Tunneling, traversal time, quantum Zeno dynamics
03.67.Lx Quantum computation architectures and implementations
05.30.Jp Boson systems
05.40.-a Fluctuation phenomena, random processes, noise, and Brownian motion
02.50.Ga Markov processes
03.65.Ta Foundations of quantum mechanics; measurement theory
03.65.Ud Entanglement and quantum nonlocality (e.g. EPR paradox, Bell's inequalities, GHZ states, etc.)

Orphan spin operators enable the acquisition of multiple 2D and 3D magic angle spinning solid-state NMR spectra

T. Gopinath and Gianluigi Veglia

J. Chem. Phys. 138, 184201 (2013); http://dx.doi.org/10.1063/1.4803126 (8 pages)

Online Publication Date: 10 May 2013

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We propose a general method that enables the acquisition of multiple 2D and 3D solid-state NMR spectra for U-13C, 15N-labeled proteins. This method, called MEIOSIS (Multiple ExperIments via Orphan SpIn operatorS), makes it possible to detect four coherence transfer pathways simultaneously, utilizing orphan (i.e., neglected) spin operators of nuclear spin polarization generated during 15N-13C cross polarization (CP). In the MEIOSIS experiments, two phase-encoded free-induction decays are decoded into independent nuclear polarization pathways using Hadamard transformations. As a proof of principle, we show the acquisition of multiple 2D and 3D spectra of U-13C, 15N-labeled microcrystalline ubiquitin. Hadamard decoding of CP coherences into multiple independent spin operators is a new concept in solid-state NMR and is extendable to many other multidimensional experiments. The MEIOSIS method will increase the throughput of solid-state NMR techniques for microcrystalline proteins, membrane proteins, and protein fibrils.
Show PACS
87.64.kj NMR
36.20.Hb Configuration (bonds, dimensions)
36.20.Kd Electronic structure and spectra
87.14.em Fibrils (amyloids, collagen, etc.)
87.14.ep Membrane proteins
87.15.B- Structure of biomolecules
87.16.dt Structure, static correlations, domains, and rafts
Author Select

A virtual-system coupled multicanonical molecular dynamics simulation: Principles and applications to free-energy landscape of protein–protein interaction with an all-atom model in explicit solvent

Junichi Higo, Koji Umezawa, and Haruki Nakamura

J. Chem. Phys. 138, 184106 (2013); http://dx.doi.org/10.1063/1.4803468 (11 pages)

Online Publication Date: 10 May 2013

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We propose a novel generalized ensemble method, a virtual-system coupled multicanonical molecular dynamics (V-McMD), to enhance conformational sampling of biomolecules expressed by an all-atom model in an explicit solvent. In this method, a virtual system, of which physical quantities can be set arbitrarily, is coupled with the biomolecular system, which is the target to be studied. This method was applied to a system of an Endothelin-1 derivative, KR-CSH-ET1, known to form an antisymmetric homodimer at room temperature. V-McMD was performed starting from a configuration in which two KR-CSH-ET1 molecules were mutually distant in an explicit solvent. The lowest free-energy state (the most thermally stable state) at room temperature coincides with the experimentally determined native complex structure. This state was separated to other non-native minor clusters by a free-energy barrier, although the barrier disappeared with elevated temperature. V-McMD produced a canonical ensemble faster than a conventional McMD method.
Show PACS
87.15.ap Molecular dynamics simulation
87.15.B- Structure of biomolecules
87.15.km Protein-protein interactions
87.80.-y Biophysical techniques (research methods)

An analytical continuation approach for evaluating emission lineshapes of molecular aggregates and the adequacy of multichromophoric Förster theory

Leonardo Banchi, Gianluca Costagliola, Akihito Ishizaki, and Paolo Giorda

J. Chem. Phys. 138, 184107 (2013); http://dx.doi.org/10.1063/1.4803694 (14 pages)

Online Publication Date: 10 May 2013

Full Text: Read Online (HTML) | Download PDF

Show Abstract
In large photosynthetic chromophore-protein complexes not all chromophores are coupled strongly, and thus the situation is well described by formation of delocalized states in certain domains of strongly coupled chromophores. In order to describe excitation energy transfer among different domains without performing extensive numerical calculations, one of the most popular techniques is a generalization of Förster theory to multichromophoric aggregates (generalized Förster theory) proposed by Sumi [J. Phys. Chem. B 103, 252 (1999)] and Scholes and Fleming [J. Phys. Chem. B 104, 1854 (2000)]. The aim of this paper is twofold. In the first place, by means of analytic continuation and a time convolutionless quantum master equation approach, a theory of emission lineshape of multichromophoric systems or molecular aggregates is proposed. In the second place, a comprehensive framework that allows for a clear, compact, and effective study of the multichromophoric approach in the full general version proposed by Jang, Newton, and Silbey [Phys. Rev. Lett. 92, 218301 (2004)] is developed. We apply the present theory to simple paradigmatic systems and we show on one hand the effectiveness of time-convolutionless techniques in deriving lineshape operators and on the other hand we show how the multichromophoric approach can give significant improvements in the determination of energy transfer rates in particular when the systems under study are not the purely Förster regime. The presented scheme allows for an effective implementation of the multichromophoric Förster approach which may be of use for simulating energy transfer dynamics in large photosynthetic aggregates, for which massive computational resources are usually required. Furthermore, our method allows for a systematic comparison of multichromophoric Föster and generalized Förster theories and for a clear understanding of their respective limits of validity.
Show PACS
87.15.bk Structure of aggregates
33.70.Jg Line and band widths, shapes, and shifts
87.14.E- Proteins
87.15.nr Aggregation

Dual effect of crowders on fibrillation kinetics of polypeptide chains revealed by lattice models

Nguyen Truong Co, Chin-Kun Hu, and Mai Suan Li

J. Chem. Phys. 138, 185101 (2013); http://dx.doi.org/10.1063/1.4804299 (5 pages)

Online Publication Date: 13 May 2013

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We have developed the lattice model for describing polypeptide chains in the presence of crowders. The influence of crowding confinement on the fibrillation kinetics of polypeptide chains is studied using this model. We observed the non-trivial behavior of the fibril formation time τfib that it decreases with the concentration of crowders if crowder sizes are large enough, but the growth is observed for crowders of small sizes. This allows us to explain the recent experimental observation on the dual effect of crowding particles on fibril growth of proteins that for a fixed crowder concentration the fibrillation kinetics is fastest at intermediate values of total surface of crowders. It becomes slow at either small or large coverages of cosolutes. It is shown that due to competition between the energetics and entropic effects, the dependence of τfib on the size of confined space is described by a parabolic function.
Show PACS
87.15.B- Structure of biomolecules
02.30.-f Function theory, analysis
36.20.Fz Constitution (chains and sequences)
87.10.Hk Lattice models
87.14.em Fibrils (amyloids, collagen, etc.)

Kinetic theory of amyloid fibril templating

Jeremy D. Schmit

J. Chem. Phys. 138, 185102 (2013); http://dx.doi.org/10.1063/1.4803658 (9 pages)

Online Publication Date: 14 May 2013

Full Text: Read Online (HTML) | Download PDF

Show Abstract
The growth of amyloid fibrils requires a disordered or partially unfolded protein to bind to the fibril and adapt the same conformation and alignment established by the fibril template. Since the H-bonds stabilizing the fibril are interchangeable, it is inevitable that H-bonds form between incorrect pairs of amino acids which are either incorporated into the fibril as defects or must be broken before the correct alignment can be found. This process is modeled by mapping the formation and breakage of H-bonds to a one-dimensional random walk. The resulting microscopic model of fibril growth is governed by two timescales: the diffusion time of the monomeric proteins, and the time required for incorrectly bound proteins to unbind from the fibril. The theory predicts that the Arrhenius behavior observed in experiments is due to off-pathway states rather than an on-pathway transition state. The predicted growth rates are in qualitative agreement with experiments on insulin fibril growth rates as a function of protein concentration, denaturant concentration, and temperature. These results suggest a templating mechanism where steric clashes due to a single mis-aligned molecule prevent the binding of additional molecules.
Show PACS
87.14.em Fibrils (amyloids, collagen, etc.)
87.15.Vv Diffusion
87.15.hp Conformational changes
87.15.Fh Bonding; mechanisms of bond breakage

A maximum entropy thermodynamics of small systems

Purushottam D. Dixit

J. Chem. Phys. 138, 184111 (2013); http://dx.doi.org/10.1063/1.4804549 (6 pages)

Online Publication Date: 14 May 2013

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We present a maximum entropy approach to analyze the state space of a small system in contact with a large bath, e.g., a solvated macromolecular system. For the solute, the fluctuations around the mean values of observables are not negligible and the probability distribution P(r) of the state space depends on the intricate details of the interaction of the solute with the solvent. Here, we employ a superstatistical approach: P(r) is expressed as a marginal distribution summed over the variation in β, the inverse temperature of the solute. The joint distribution P(β, r) is estimated by maximizing its entropy. We also calculate the first order system-size corrections to the canonical ensemble description of the state space. We test the development on a simple harmonic oscillator interacting with two baths with very different chemical identities, viz., (a) Lennard-Jones particles and (b) water molecules. In both cases, our method captures the state space of the oscillator sufficiently well. Future directions and connections with traditional statistical mechanics are discussed.
Show PACS
05.70.Ce Thermodynamic functions and equations of state
05.40.-a Fluctuation phenomena, random processes, noise, and Brownian motion
05.20.Jj Statistical mechanics of classical fluids
02.50.Cw Probability theory

Coarse-grain simulations of active molecular machines in lipid bilayers

Mu-Jie Huang, Raymond Kapral, Alexander S. Mikhailov, and Hsuan-Yi Chen

J. Chem. Phys. 138, 195101 (2013); http://dx.doi.org/10.1063/1.4803507 (11 pages)

Online Publication Date: 15 May 2013

Full Text: Read Online (HTML) | Download PDF

Show Abstract
A coarse-grain method for simulations of the dynamics of active protein inclusions in lipid bilayers is described. It combines the previously proposed hybrid simulations of bilayers [M.-J. Huang, R. Kapral, A. S. Mikhailov, and H.-Y. Chen, J. Chem. Phys. 137, 055101 (2012)], based on molecular dynamics for the lipids and multi-particle collision dynamics for the solvent, with an elastic-network description of active proteins. The method is implemented for a model molecular machine which performs active conformational motions induced by ligand binding and its release after reaction. The situation characteristic for peripheral membrane proteins is considered. Statistical investigations of the effects of single active or passive inclusions on the shape of the membrane are carried out. The results show that the peripheral machine produces asymmetric perturbations of the thickness of two leaflets of the membrane. It also produces a local saddle in the midplane height of the bilayer. Analysis of the power spectrum of the fluctuations of the membrane midplane shows that the conformational motion of the machine perturbs these membrane fluctuations. The hydrodynamic lipid flows induced by cyclic conformational changes in the machine are analyzed. It is shown that such flows are long-ranged and should provide an additional important mechanism for interactions between active inclusions in biological membranes.
Show PACS
87.15.hp Conformational changes
87.15.kp Protein-ligand interactions
87.15.kt Protein-membrane interactions
87.16.dj Dynamics and fluctuations
87.16.dm Mechanical properties and rheology
87.15.ap Molecular dynamics simulation

Confined Brownian ratchets

Paolo Malgaretti, Ignacio Pagonabarraga, and J. Miguel Rubi

J. Chem. Phys. 138, 194906 (2013); http://dx.doi.org/10.1063/1.4804632 (9 pages)

Online Publication Date: 21 May 2013

Full Text: Read Online (HTML) | Download PDF

Show Abstract
We analyze the dynamics of Brownian ratchets in a confined environment. The motion of the particles is described by a Fick-Jakobs kinetic equation in which the presence of boundaries is modeled by means of an entropic potential. The cases of a flashing ratchet, a two-state model, and a ratchet under the influence of a temperature gradient are analyzed in detail. We show the emergence of a strong cooperativity between the inherent rectification of the ratchet mechanism and the entropic bias of the fluctuations caused by spatial confinement. Net particle transport may take place in situations where none of those mechanisms leads to rectification when acting individually. The combined rectification mechanisms may lead to bidirectional transport and to new routes to segregation phenomena. Confined Brownian ratchets could be used to control transport in mesostructures and to engineer new and more efficient devices for transport at the nanoscale.
Show PACS
05.40.Jc Brownian motion
05.70.Ce Thermodynamic functions and equations of state
05.60.-k Transport processes

Dynamics simulation of the interaction between serine and water

Yang Liu, Peng Zhang, Ying-Bo Lu, Sheng-Hao Han, and Hui Yu

J. Chem. Phys. 138, 205101 (2013); http://dx.doi.org/10.1063/1.4807004 (5 pages)

Online Publication Date: 23 May 2013

Full Text: Read Online (HTML) | Download PDF

Show Abstract
Using the first principles density functional theory (DFT), we simulated the neutron scattering spectra of the hydration dynamics of serine. Experimental data analyses have shown that dissociative H2O molecules were more likely to form hydrogen bonds (H-bonds) with an –OH group in monohydrated serine and easily shift to a –NH3+ group at a higher hydration level [P. Zhang, Y. Zhang, S. H. Han, Q. W. Yan, R. C. Ford, and J. C. Li, J. Phys. Chem. A 110, 5000 (2006)]. We set the 1:1 ratio hydrated compounds at the two positions and found that the H2O could be optimized to form H-bonds with –OH and –NH3+ separately. When the simulated phonon signals of the –OH…H2O and –NH3+…H2O combinations were summed on a 3:1 scale, the calculating spectra were in good agreement with the experimental results, especially for the peak at 423 cm−1 of the –OH…H2O combination and the peak at 367 cm−1 of the –NH3+…H2O combination, which mutually complemented the real spectrum. We confirm that H2O may break the intermolecular H-bonds of the interlaced binding –OH to form a new structure, and that with the skeleton deformation of serine, H2O forms stronger H-bonds more often with the –NH3+ side indicating the flexible dynamic mechanism of the serine hydration process.
Show PACS
87.15.hg Dynamics of intermolecular interactions
31.15.E- Density-functional theory
87.15.ap Molecular dynamics simulation
87.15.Fh Bonding; mechanisms of bond breakage
82.30.Rs Hydrogen bonding, hydrophilic effects
33.15.Fm Bond strengths, dissociation energies

Kinetics of molecular transitions with dynamic disorder in single-molecule pulling experiments

Yue Zheng, Ping Li, Nanrong Zhao, and Zhonghuai Hou

J. Chem. Phys. 138, 204102 (2013); http://dx.doi.org/10.1063/1.4801331 (8 pages)

Online Publication Date: 23 May 2013

Full Text: Read Online (HTML) | Download PDF

Show Abstract
Macromolecular transitions are subject to large fluctuations of rate constant, termed as dynamic disorder. The individual or intrinsic transition rates and activation free energies can be extracted from single-molecule pulling experiments. Here we present a theoretical framework based on a generalized Langevin equation with fractional Gaussian noise and power-law memory kernel to study the kinetics of macromolecular transitions to address the effects of dynamic disorder on barrier-crossing kinetics under external pulling force. By using the Kramers’ rate theory, we have calculated the fluctuating rate constant of molecular transition, as well as the experimentally accessible quantities such as the force-dependent mean lifetime, the rupture force distribution, and the speed-dependent mean rupture force. Particular attention is paid to the discrepancies between the kinetics with and without dynamic disorder. We demonstrate that these discrepancies show strong and nontrivial dependence on the external force or the pulling speed, as well as the barrier height of the potential of mean force. Our results suggest that dynamic disorder is an important factor that should be taken into account properly in accurate interpretations of single-molecule pulling experiments.
Show PACS
82.20.Pm Rate constants, reaction cross sections, and activation energies
82.20.Uv Stochastic theories of rate constants
82.37.Np Single molecule reaction kinetics, dissociation, etc.
82.20.Db Transition state theory and statistical theories of rate constants

Instantaneous normal mode analysis of the vibrational relaxation of the amide I mode of alanine dipeptide in water

Marwa H. Farag, José Zúñiga, Alberto Requena, and Adolfo Bastida

J. Chem. Phys. 138, 205102 (2013); http://dx.doi.org/10.1063/1.4805086 (13 pages)

Online Publication Date: 24 May 2013

Full Text: Read Online (HTML) | Download PDF

Show Abstract
Nonequilibrium Molecular Dynamics (MD) simulations coupled to instantaneous normal modes (INMs) analysis are used to study the vibrational relaxation of the acetyl and amino-end amide I modes of the alanine dipeptide (AlaD) molecule dissolved in water (D2O). The INMs are assigned in terms of the equilibrium normal modes using the Effective Atomic Min-Cost algorithm as adapted to make use of the outputs of standard MD packages, a method which is well suited for the description of flexible molecules. The relaxation energy curves of both amide I modes show multiexponential decays, in good agreement with the experimental findings. It is found that ∼85%–90% of the energy relaxes through intramolecular vibrational redistribution. The main relaxation pathways are also identified. The rate at which energy is transferred into the solvent is similar for the acetyl-end and amino-end amide I modes. The conformational changes occurring during relaxation are investigated, showing that the populations of the alpha and beta region conformers are altered by energy transfer in such a way that it takes 15 ps for the equilibrium conformational populations to be recovered after the initial excitation of the AlaD molecule.
Show PACS
31.15.xv Molecular dynamics and other numerical methods
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.20.Tp Vibrational analysis
34.20.Gj Intermolecular and atom-molecule potentials and forces
back to top
RSS Feeds
FREE

Erratum: “Accelerating atomic-level protein simulations by flat-histogram techniques” [J. Chem. Phys. 135, 125102 (2011)]

Sigurður Æ. Jónsson, Sandipan Mohanty, and Anders Irbäck

J. Chem. Phys. 138, 189902 (2013); http://dx.doi.org/10.1063/1.4806968 (1 page)

Online Publication Date: 10 May 2013

Full Text: Read Online (HTML) | Download PDF

Abstract Unavailable
Show PACS
99.10.Cd Errata
87.15.A- Theory, modeling, and computer simulation
36.20.-r Macromolecules and polymer molecules
87.14.E- Proteins
Close
ADVERTISEMENT

Go to AIP Home   © AIP Publishing LLC
close