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19942026
most citedParallel Tempering Algorithm for Conformational Studies of Biological Molecules

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24 papers · 1 filter

cond-mat.soft2025★ 2 cited

Kinetic phase diagram for two-step nucleation in colloid-polymer mixtures

Willem Gispen, Peter G. Bolhuis, Marjolein Dijkstra

Two-step crystallization via a metastable intermediate phase is often regarded as a non-classical process that lies beyond the framework of classical nucleation theory (CNT). In th…

cond-mat.soft2024★ 10 cited

Unraveling the dynamic slowdown in supercooled water: The role of dynamic disorder in jump motions

Shinji Saito

When a liquid is rapidly cooled below its melting point without inducing crystallization, its dynamics slow down significantly without noticeable structural changes. Elucidating th…

cond-mat.soft2019★ 20 cited

Diffusion dynamics of supercooled water modeled with the cage-jump motion and hydrogen-bond rearrangement

Takuma Kikutsuji, Kang Kim, Nobuyuki Matubayasi

The slow dynamics of glass-forming liquids is generally ascribed to the cage-jump motion. In the cage-jump picture, a molecule remains in a cage formed by neighboring molecules, an…

cond-mat.soft2019★ 16 cited

Classification of mobile- and immobile-molecule timescales for the Stokes-Einstein and Stokes-Einstein-Debye relations in supercooled water

Takeshi Kawasaki, Kang Kim

Molecular dynamics simulations have been performed on TIP4P/2005 supercooled water to investigate the molecular diffusion and shear viscosity at various timescales and assess the S…

cond-mat.soft2018★ 58 cited

Crucial role of fragmented and isolated defects in persistent relaxation of deeply supercooled water

Shinji Saito, Biman Bagchi, Iwao Ohmine

Properties of water have been well elucidated for temperatures above 230 K and yet mysteries remain in the deeply supercooled region. By performing extensive molecular dynami…

cond-mat.soft2018

Exploration of vitrification of water and Kauzmann entropy through complex specific heat: A journey through 'No Man's Land'

Shinji Saito, Biman Bagchi

Frequency dependent specific heat, introduced by Grest and Nagel, offers valuable insight into the vitrification of supercooled liquid. We calculate this quantity and other thermod…

cond-mat.soft2018★ 46 cited

Spurious violation of the Stokes-Einstein-Debye relation in supercooled water

Takeshi Kawasaki, Kang Kim

The theories of Brownian motion, the Debye rotational diffusion model, and hydrodynamics together provide us with the Stokes--Einstein--Debye (SED) relation between the rotational…

cond-mat.soft2016★ 17 cited

Anomalous dimensionality dependence of diffusion in a rugged energy landscape : How pathological is one dimension ?

Kazuhiko Seki, Kaushik Bagchi, Biman Bagchi

Rugged (or, rough) energy landscape (REL) with spatially distributed maxima and minima are often employed in applications of physics, chemistry and biology (enzyme kinetics, protei…

cond-mat.soft2013★ 28 cited

Frequency dependence of specific heat in supercooled liquid water and emergence of correlated dynamics

Shinji Saito, Iwao Ohmine, Biman Bagchi

Molecular origin of the well-known specific heat anomaly in supercooled liquid water is investigated here by using extensive computer simulations and theoretical analyses. A rather…

cond-mat.soft2012★ 83 cited

Multiple length and time scales of dynamic heterogeneities in model glass-forming liquids: A systematic analysis of multi-point and multi-time correlations

Kang Kim, Shinji Saito

We report an extensive and systematic investigation of the multi-point and multi-time correlation functions to reveal the spatio-temporal structures of dynamic heterogeneities in g…

cond-mat.soft2010★ 49 cited

Multi-time density correlation functions in glass-forming liquids: Probing dynamical heterogeneity and its lifetime

Kang Kim, Shinji Saito

A multi-time extension of a density correlation function is introduced to reveal temporal information about dynamical heterogeneity in glass-forming liquids. We utilize a multi-tim…

cond-mat.soft2009★ 33 cited

Multiple time scales hidden in heterogeneous dynamics of glass-forming liquids

Kang Kim, Shinji Saito

A multi-time probing of density fluctuations is introduced to investigate hidden time scales of heterogeneous dynamics in glass-forming liquids. Molecular dynamics simulations for…

cond-mat.soft2009★ 73 cited

Slow dynamics in random media: Crossover from glass to localization transition

Kang Kim, Kunimasa Miyazaki, Shinji Saito

We study slow dynamics of particles moving in a matrix of immobile obstacles using molecular dynamics simulations. The glass transition point decreases drastically as the obstacle…

cond-mat.soft2008★ 18 cited

Nonequilibrium mode-coupling theory for uniformly sheared systems

Song-Ho Chong, Bongsoo Kim

We develop a nonequilibrium mode-coupling theory for uniformly sheared systems starting from microscopic, thermostatted SLLOD equations of motion. Our theory aims at describing sta…

cond-mat.soft2008★ 105 cited

Coupling/decoupling between translational and rotational dynamics in a supercooled molecular liquid

Song-Ho Chong, Walter Kob

We use molecular dynamics computer simulations to investigate the coupling/decoupling between translational and rotational dynamics in a glass-forming liquid of dumbbells. This is…

cond-mat.soft2008★ 74 cited

Connections of activated hopping processes with the breakdown of the Stokes-Einstein relation and with aspects of dynamical heterogeneities

Song-Ho Chong

We develop a new extended version of the mode-coupling theory (MCT) for glass transition, which incorporates activated hopping processes via the dynamical theory originally formula…

cond-mat.soft2007★ 42 cited

Structural and conformational dynamics of supercooled polymer melts: Insights from first-principles theory and simulations

Song-Ho Chong, Martin Aichele, Hendrik Meyer +2

We report on quantitative comparisons between simulation results of a bead-spring model and mode-coupling theory calculations for the structural and conformational dynamics of a su…

cond-mat.soft2007★ 141 cited

Optical Properties of Pentacene and Perfluoropentacene Thin Films

Alexander Hinderhofer, Ute Heinemeyer, Alexander Gerlach +5

The optical properties of pentacene (PEN) and perfluoropentacene(PFP) thin films on various SiO2 substrates were studied using variable angle spectroscopic ellipsometry. Structural…

cond-mat.soft2006★ 19 cited

Role of structural relaxations and vibrational excitations in the high-frequency dynamics of liquids and glasses

Song-Ho Chong

We present theoretical investigation on the high-frequency collective dynamics in liquids and glasses at microscopic length scales and terahertz frequency region based on the mode-…

cond-mat.soft2006★ 1 cited

On the role of hydrodynamic interactions in colloidal gelation

R. Yamamoto, K. Kim, Y. Nakayama +2

In this letter, we investigate several aspects related to the effect of hydrodynamics interactions on phase separation-induced gelation of colloidal particles. We explain physicall…

cond-mat.soft2006★ 101 cited

Simulating (electro)hydrodynamic effects in colloidal dispersions: smoothed profile method

Yasuya Nakayama, Kang Kim, Ryoichi Yamamoto

Previously, we have proposed a direct simulation scheme for colloidal dispersions in a Newtonian solvent [Phys.Rev.E 71,036707 (2005)]. An improved formulation called the ``Smoothe…

cond-mat.soft2005★ 39 cited

Dynamics in a supercooled liquid of symmetric dumbbells: Reorientational hopping for small molecular elongations

Angel J. Moreno, Song-Ho Chong, Walter Kob +1

We present extensive molecular dynamics simulations of a liquid of symmetric dumbbells, for constant packing fraction, as a function of temperature and molecular elongation. For la…

cond-mat.soft2005★ 65 cited

Evidence for the weak steric hindrance scenario in the supercooled-state reorientational dynamics

S. -H. Chong, A. J. Moreno, F. Sciortino +1

We use molecular-dynamics computer simulations to study the translational and reorientational dynamics of a glass-forming liquid of dumbbells. For sufficiently elongated molecules…

cond-mat.soft2002★ 27 cited

Polyhedral vesicles

Hiroshi Noguchi

Polyhedral vesicles with a large bending modulus of the membrane such as the gel phase lipid membrane were studied using a Brownian dynamics simulation. The vesicles exhibit variou…