Article
Chemistry, Physical
Luis Perez-Mas, Maria del Mar Ramos-Tejada, Alberto Martin-Molina, Jose-Alberto Maroto-Centeno, Manuel Quesada-Perez
Summary: In this study, we use coarse-grained simulations to investigate how electrostatic forces affect the diffusion of solute in flexible gels. The model considers the movement of solute particles and polyelectrolyte chains and uses a Brownian dynamics algorithm. We analyze the impact of three electrostatic parameters on the system. Our findings reveal that changes in the electric charge of the species influence both the diffusion coefficient and the anomalous diffusion exponent. We also observe differences in the diffusion coefficient between flexible and rigid gels, particularly at low ionic strength. Additionally, the flexibility of the chains significantly affects the exponent of anomalous diffusion, even at high ionic strength (100 mM). Our simulations demonstrate that altering the charge of the polyelectrolyte chains does not have the same effect as changing the charge of the solute particles.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Thorsten Prustel, Martin Meier-Schellersheim
Summary: This study focused on computational models of reaction-diffusion systems commonly found in cellular signaling pathways, and introduced an approach that allows for the reconstruction of entire molecular trajectories after a simulated time step, avoiding the need for inefficient draws from non-standard distributions. This method enables highly accurate stochastic simulations for system sizes that would be prohibitively costly to simulate with conventional Green's function based methods.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Mechanics
Kyunil Rah
Summary: Apart from describing the transport behaviors to a reliable accuracy, it remains as yet far from satisfactory to comprehend the explicit role of the solvent-colloid interaction on the diffusivity and viscosity of colloidal hard-sphere suspensions. In this study, we use statistical mechanics to investigate the influence of the free volume effect on the diffusivity and viscosity. The theory predicts a crossover in the solvent effect on the diffusivity, with the solvent-colloid interaction either enhancing or inhibiting diffusion depending on the colloidal concentration.
Article
Physics, Multidisciplinary
Pierre Rizkallah, Alessandro Sarracino, Olivier Benichou, Pierre Illien
Summary: In this study, the diffusion coefficient of an active tracer in a crowded environment with hardcore interactions is calculated. A closure approximation method is proposed to accurately determine the diffusion coefficient for an arbitrary density of crowders in the system, capturing non-equilibrium effects. The approach also allows the characterization of environment perturbations induced by the movement of the active tracer. The asymptotic regimes of low and high densities are considered to obtain explicit expressions for the diffusion coefficient.
PHYSICAL REVIEW LETTERS
(2022)
Article
Physics, Fluids & Plasmas
Baruch Meerson
Summary: We evaluated the mean escape time of overdamped particles over potential barriers in short-correlated quenched Gaussian disorder potentials in one dimension at low temperature. The form of the tail of the potential barrier probability distribution has a significant impact on the thermally activated escape. We used the optimal fluctuation method to evaluate this tail. We found that for monotone decreasing autocovariances, the obtained tail is consistent with the result obtained by Lopatin and Vinokur (2001). However, for nonmonotonic autocovariances with negative autocorrelations, we observed a higher tail, leading to an exponential increase in the mean escape time. The transition between the two regimes exhibits characteristics of a first-order transition.
Article
Mechanics
Long Gao, Junhao Peng, Chunming Tang, A. P. Riascos
Summary: This paper investigates biased random walks on weighted scale-free trees, analyzing the trapping efficiency through average trapping time (ATT) and global mean first-passage times (GMFPT) metrics, and explores the impact of parameter w on trapping efficiency. The results suggest that in non-fractal scenarios, lower values of w lead to higher ATT, while proper settings of w can enhance trapping efficiency on fractal trees. Additionally, the highest trapping efficiency is observed in unweighted networks for the non-fractal case, with a reduction in trapping frequency for other values of w.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2021)
Article
Chemistry, Multidisciplinary
Robin Kueng, Anne Germann, Marcel Kruesmann, Louisa P. Niggemann, Jan Meisner, Matthias Karg, Robert Goestl, Bernd M. Schmidt
Summary: We have developed metal-organic cage-crosslinked polymer hydrogels by using bipyridine-functionalized polyethylene glycol chains. These hydrogels can encapsulate guest molecules and can be disassembled by ultrasound to release the cargo. The performance of the hydrogels was characterized by various techniques, including NMR, rheology, and SAXS experiments. The study also reveals the mechanism of cage-opening and demonstrates the enhanced drug-loading capacity of the hydrogels compared to non-crosslinked assemblies.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Physics, Multidisciplinary
Yi-Qi Xia, Guo-Qiang Feng, Zhuang-Lin Shen
Summary: We design a nunchakus-like tracer and investigate its self-adaptive behavior in an active Brownian particle (ABP) bath by adjusting the self-propelled capability and density of ABPs. The tracer maintains a stable wedge-like shape when the self-propelled force is high enough, and the angle between the two arms and the velocity of the joint point are analyzed. The results show a non-monotonic relationship between the angle and the active force, while it increases monotonically with the density of ABPs. We also find a linear relationship between the velocity and the self-propelled force under high activity, and the tracer can flip at high density of ABPs.
Article
Physics, Multidisciplinary
Vincent Rossetto
Summary: This paper examines the solutions of the radiative transfer equation and their relationship with Green's functions, suggesting that the transitivity property can be achieved by considering the radiance distribution in phase space. Exact solutions are obtained in one and two dimensions using continuous-time persistent random walks, which correspond to the Fokker-Planck equation of the radiative transfer equation. The Lorentz covariance property is confirmed, and the measured signal from a pulse source in one dimension is discussed, unveiling an effective random delay when the pulse is emitted away from the observer.
Article
Chemistry, Physical
Raffaele Pastore, Takuma Kikutsuji, Francesco Rusciano, Nobuyuki Matubayasi, Kang Kim, Francesco Greco
Summary: The breakdown of Stokes-Einstein relation in supercooled liquids is attributed to dynamic heterogeneities, but a clear microscopic interpretation is still lacking. Research shows a proportional relationship between tau(alpha)/tau(D) and < t(p)>/< t(c) in supercooled liquids, connecting macroscopic and microscopic timescales. This study provides a microscopic perspective on the Stokes-Einstein breakdown and extends previous results to more realistic glass-formers.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Physics, Fluids & Plasmas
Igor Goychuk, Thorsten Poschel
Summary: Experimental studies have shown subdiffusion of nanoparticles in various environments, combining features of both viscoelasticity and non-Markovian diffusional processes. The viscoelastic subdiffusion approach in random environments based on Langevin dynamics provides a more rational explanation for these findings compared to earlier proposed theories.
Article
Physics, Multidisciplinary
Hidde D. Vuijk, Holger Merlitz, Michael Lang, Abhinav Sharma, Jens-Uwe Sommer
Summary: Active particles, when bound to passive objects, exhibit chemotaxis and move towards regions of higher activity. Connecting active particles into chains can lead to a transition from antichemotaxis to chemotaxis, allowing protoforms of life to locate sources of nutrients without sensory-motor apparatus.
PHYSICAL REVIEW LETTERS
(2021)
Article
Mechanics
P. M. Ndiaye, F. W. Tavares, E. K. Lenzi, L. R. Evangelista, H. Ribeiro, D. Marin, L. M. S. Guilherme, R. S. Zola
Summary: The study focuses on the modeling of diffusion and trapping of particles inspired by biology and natural behavior, particularly in systems connected by surfaces to bulk, such as living cells and biomaterials. The research finds a variety of behaviors through analytical calculations and computer simulations, showing a good agreement between the two methods.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2021)
Article
Mechanics
Pavel Castro-Villarreal, Claudio Contreras-Aburto, Sendic Estrada-Jimenez, Idrish Huet-Hernandez, Oscar Vazquez-Rodriguez
Summary: The study examines the stochastic dynamics of a tagged Brownian particle in an interacting system using the path-integral representation and contrasts it with the standard equations. It investigates the single-file diffusion phenomenon and the mean-square displacement of the tracer particle in terms of Bessel functions. Additionally, it explores the behavior of a Brownian particle system with paramagnetic interactions near crystallization using a perturbation treatment and validates the findings through Brownian dynamics simulation.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2021)
Article
Physics, Applied
Drew Lilley, Anubhav Jain, Ravi Prasher
Summary: The analytical model presented in this study calculates the entropy at melt of monatomic liquids by considering a rough potential energy surface. It offers a simple explanation for Richard's melting rule and provides a material-dependent correction to Trouton's vaporization rule. When combined with the phonon theory of liquids, it allows for estimation of entropy over the entire liquid range without adjustable parameters.
APPLIED PHYSICS LETTERS
(2021)
Article
Chemistry, Physical
Minjung Kim, Eunji Kim, Seunghoon Lee, Jun Soo Kim, Sangyoub Lee
JOURNAL OF PHYSICAL CHEMISTRY A
(2019)
Article
Chemistry, Physical
Seulki Kwon, Seulgi Lee, Hyun Woo Cho, Jeongmin Kim, Jun Soo Kim, Bong June Sung
JOURNAL OF CHEMICAL PHYSICS
(2019)
Article
Multidisciplinary Sciences
Suehyun Park, Jeongeun Song, Jun Soo Kim
Article
Chemistry, Multidisciplinary
Hye Jin Lee, U. Leong Yang, Kyeong Nam Kim, Soojin Park, Kye Hyoung Kil, Jun Soo Kim, Alec M. Wodtke, Won Jun Choi, Myung Hwa Kim, Jeong Min Baik
Article
Multidisciplinary Sciences
Sanggeun Song, Seong Jun Park, Minjung Kim, Jun Soo Kim, Bong June Sung, Sangyoub Lee, Ji-Hyun Kim, Jaeyoung Sung
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Chemistry, Multidisciplinary
Sehui Bae, Inrok Oh, Jejoong Yoo, Jun Soo Kim
Summary: Flexibility of DNA plays a crucial role in the complex formation with cationic nanoparticles, as demonstrated through molecular dynamics simulations. A small increase in DNA persistence length by 10 nm requires a significantly increased electric charge of the nanoparticle for wrapping. Greater DNA flexibility results in bending and wrapping around nanoparticles with intermediate electric charges, while less flexible DNA binds without notable bending.
Article
Chemistry, Physical
Sehui Bae, Jun Soo Kim
Summary: Research on wrapping DNA double helix around cationic nanoparticles using potential of mean force (PMF) shows thermodynamic preference for complex formation with more flexible DNA. Furthermore, utilizing sequence-dependent DNA flexibility in DNA nanotechnologies is suggested for regulating nanoparticle dynamics and triggering structural transformations.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Multidisciplinary Sciences
Minjung Kim, Jun Soo Kim
Summary: A new cascading failure model describing the probability of failure of overloaded nodes was proposed, with simulations showing robustness differences depending on initial load distribution and load redistribution. The optimal load distribution results were verified through theoretical analysis, aiding in developing effective mitigation measures and designing robust networks.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Multidisciplinary
Minjung Kim, Chi Cheng Hong, Saeyeon Lee, Jun Soo Kim
Summary: In this study, we investigated the dynamics of a 90-base pair-long DNA minicircle with the sequence of (AT)(45)/(AT)(45) using all-atom molecular dynamics simulation. Our analysis of poloidal rotation and in-plane circular vibration revealed the highly dynamic internal motion of the small DNA minicircle.
BULLETIN OF THE KOREAN CHEMICAL SOCIETY
(2022)
Article
Physics, Fluids & Plasmas
Inrok Oh, Jeongeun Song, Hye Ree Hyun, Sang Hak Lee, Jun Soo Kim
Summary: This study proposes a method of directional transport of nanometer-sized particles along DNA by adjusting the flexibility gradient of DNA. Experimental results show that stretching and relaxation of the DNA molecule can tune the asymmetric potentials for DNA-nanoparticle binding, leading to directional movement of nanometer-sized particles.
Article
Chemistry, Physical
Hye Ree Hyun, Jungim Han, Juhyung Lim, Young Jae Park, Byoungki Choi, Chul Baik, Jun Soo Kim
Summary: This study investigates the liquid-like properties of cyclopentadienyl barium complexes in nanoscale droplets using molecular dynamics simulations. The results show that substituting different alkyl and silyl groups significantly affects the structure and dynamics of the compounds, with silyl groups interacting more softly than tert-butyl groups.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Minjung Kim, Sehui Bae, Inrok Oh, Jejoong Yoo, Jun Soo Kim
Summary: This study investigates the sequence-dependent coupling between DNA bending and its helical twist, identifying specific dinucleotide steps with strong twist-bend coupling during DNA minicircle formation. This work provides new insights into the structural responses of DNA to mechanical deformation, particularly in sharply bent DNA minicircles, for nanoscale applications.
Article
Physics, Fluids & Plasmas
Kye Hyoung Kil, Arun Yethiraj, Jun Soo Kim
Article
Chemistry, Multidisciplinary
Ji-eun Park, Myungjoo Seo, Eunseon Jang, Haein Kim, Jun Soo Kim, So-Jung Park