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Mesoscopic simulations of polyelectrolyte electrophoresis in nanochannels
[article]
2010
arXiv
pre-print
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We present the results of mesoscopic dissipative particle dynamics (DPD) simulations of coupled electrohydrodynamic phenomena on the micro- and nanoscale. The effects of electroosmotic flow and slippage combined with polyelectrolyte electrophoresis are investigated in detail, taking full account of hydrodynamic and electrostatic interactions. Our numerical results are in excellent agreement with analytical calculations.
arXiv:1007.3585v1
fatcat:bnq72tykr5asvopzz4yiy4xsgm
Screening of hydrodynamic interactions for polyelectrolytes in salt solution
[article]
2008
arXiv
pre-print
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We provide numerical evidence that hydrodynamic interactions are screened for charged polymers in salt solution on time scales below the Zimm time. At very short times, a crossover to hydrodynamic behavior is observed. Our conclusions are drawn from extensive coarse-grained computer simulations of polyelectrolytes in explicit solvent and explicit salt, and discussed in terms of analytical arguments based on the Debye-Hueckel approximation.
arXiv:0809.5239v1
fatcat:r5ldvbj73basfl4d75svz2zroe
Macromolecular unfolding properties in presence of compatible solutes
[article]
2011
arXiv
pre-print
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We present Molecular Dynamics simulations of Chymotrypsin inhibitor II and PEO in presence of compatible solutes. Our results indicate that the the native compact state of the studied macromolecules is stabilized in presence of hydroxyectoine. We are able to explain the corresponding mechanism by a variation of the solvent properties for higher hydroxyectoine concentrations. Our results are validated by detailed free energy calculations.
arXiv:1110.2958v1
fatcat:xnaxqc7qyveflgmbonybyylnka
Separation of chiral particles in micro- or nanofluidic channels
[article]
2012
arXiv
pre-print
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We propose a method to separate enantiomers in microfluidic or nanofluidic channels. It requires flow profiles which break chiral symmetry and have regions with high local shear. Such profiles can be generated in channels confined by walls with different hydrodynamic boundary conditions (e.g. slip lengths). Due to a nonlinear hydrodynamic effect, particles with different chirality migrate at different speed and can be separated. The mechanism is demonstrated by computer simulations. We
arXiv:1204.4079v1
fatcat:n5jw46w3ybehrlunlpy2bq2otu
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... te the influence of thermal fluctuations (i.e. the P\'eclet number) and show that the effect disappears in the linear response regime. The details of the microscopic flow are important and determine which volume forces are necessary to achieve separation.
High temperature unfolding simulations of a single stranded DNA i-motif
[article]
2011
arXiv
pre-print
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We present the results of high temperature 500 K Molecular Dynamics simulations of the DNA i-motif. The essential dynamics and the main unfolding pathways are compared to a biased metadynamics simulation at 300 K. Our results indicate a remarkable agreement of the concerted motion at both temperatures. The transition can be described by a few number of eigenvectors indicating a simple unfolding process. Two main mechanisms for the unfolding pathway at 500 K can be detected which are in good
arXiv:1103.5932v1
fatcat:5lfuzwem6vairbgxwstk57bbya
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... ement to the results of the biased simulation at 300 K.
Hidden complexities in the unfolding mechanism of a cytosine-rich DNA strand
[article]
2011
arXiv
pre-print
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We investigate the unfolding pathway of a cytosine-rich DNA hairpin structure via Molecular Dynamics simulations. Our results indicate a hidden complexity present in the unfolding process. W e show that this complex behavior arises due to non-stochastic contributions which have an important impact on the description of the dynamics in terms of collective variables.
arXiv:1109.5474v1
fatcat:62upvgqn6vb3xljmqjrq5nouni
Aqueous ionic liquids in comparison with standard co-solutes
2018
Biophysical Reviews
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Jens Smiatek declares that he has no conflicts of interest. Ethical approval This article does not contain any studies with human participants or animals performed by any of the authors. ...
Previous findings by others and us (Smiatek 2014; Micciulla et al. 2016; Schroer et al. 2016; Horinek and Netz 2011 ; Rodríguez-Ropero and van der Vegt 2015; Oprzeska-Zingrebe and Smiatek 2018) highlighted ...
doi:10.1007/s12551-018-0414-7
pmid:29611033
pmcid:PMC5988629
fatcat:byjjaxkyczcclfadnwvp63vjyi
Calculation of free energy landscapes: A Histogram Reweighted Metadynamics approach
[article]
2011
arXiv
pre-print
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We present an efficient method for the calculation of free energy landscapes. Our approach involves a history dependent bias potential which is evaluated on a grid. The corresponding free energy landscape is constructed via a histogram reweighting procedure a posteriori. Due to the presence of the bias potential, it can be also used to accelerate rare events. In addition, the calculated free energy landscape is not restricted to the actual choice of collective variables and can in principle be
arXiv:1006.4308v2
fatcat:ud4a7wohujgyljb2m45tdy5gum
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... xtended to auxiliary variables of interest without further numerical effort. The applicability is shown for several examples. We present numerical results for the alanine dipeptide and the Met-Enkephalin in explicit solution to illustrate our approach. Furthermore we derive an empirical formula that allows the prediction of the computational cost for the ordinary metadynamics variant in comparison to our approach which is validated by a dimensionless representation.
Energetic Arguments on the Microstructural Analysis in Ionic Liquids
2021
Advanced Theory and Simulations
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The interaction of ionic liquids (ILs) with additives or impurities is crucial for the performance of ILs in technological applications. In order to understand the interaction between these, an insight onto the microscopic arrangement of molecules is needed. As a representative case, 1-ethyl-3-methylimidazolium dicyanamide ( [EMIM] + [DCA] − ) mixtures are studied with dimethyl sulfoxide (DMSO) and water in bulk phase using molecular dynamics (MD) simulations. Different molar fractions of DMSO
doi:10.1002/adts.202100114
fatcat:ggbyxatclbfyjdfpqkj7qhmmzq
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... nd water are studied to elucidate the influence of the molecular solute concentration on the structuring of the ILs. The results indicate that DMSO-[EMIM] + [DCA] and water-[EMIM] + [DCA] − mixtures are defined by quite distinct molecular interactions between the species. By increasing the DMSO or water concentration, in the former the solute molecules are repelled from the ions, while in the latter they accumulate closer to the ions. The differences arise from the weakening of the interactions between the ions imposed by the presence of the water molecules whereas DMSO promotes a strengthening of these interactions. Accordingly, this study provides a deep understanding of the IL behavior in combination with neutral solute molecules and allows for a proper selection of IL-solute combinations in view of specific technological applications.
Unfolding mechanism and the free energy landscape of a single stranded DNA i-motif
[article]
2011
arXiv
pre-print
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We present Molecular Dynamics simulations of a single stranded unprotonated DNA i-motif in explicit solvent. Our results indicate that the native structure in non-acidic solution at 300 K is unstable and completely vanishes on a time scale up to 10 ns. Two unfolding mechanisms with decreasing connectivity between the initially interacting nucleobases can be identified where one pathway is characterized as entropically more favorable. The entropic preference can be mainly explained by strong
arXiv:1105.3894v1
fatcat:i4lrb4rj4beqjbplkwczxoansu
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... r ordering effects due to hydrogen bonds for several occurring structures along the pathways. Finally we are able to indicate via free energy calculations the most stable configurations belonging to distinct hairpin structures in good agreement to experimental results.
A statistical view on team handball results: home advantage, team fitness and prediction of match outcomes
[article]
2012
arXiv
pre-print
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Smiatek for helpful and inspiring discussions. ...
arXiv:1207.0700v1
fatcat:x2g56snamrhttdxafzjxwpw4ze
Low concentrated hydroxyectoine solutions in presence of DPPC lipid bilayers: a computer simulation study
[article]
2013
arXiv
pre-print
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The influence of hydroxyectoine on the properties of the aqueous solution in presence of DPPC lipid bilayers is studied via semi-isotropic constant pressure (NPT) Molecular Dynamics simulations. We investigate the solvent-co-solute behavior in terms of Kirkwood-Buff integrals as well as hydrogen bond life times for an increasing hydroxyectoine concentration up to 0.148 mol/L. The observed preferential exclusion mechanism identifies hydroxyectoine as a kosmotropic osmolyte. Our findings in
arXiv:1305.3563v1
fatcat:ayq3py35wzgcnjgi3s6qagp2g4
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... s to the DPPC lipid bilayer indicate an increase of the surface pressure as well as the solvent accessible surface area in presence of higher hydroxyectoine concentrations. The results are in agreement to the outcome of recent experiments. With this study, we are able to validate the visibility of co-solute-solute-solvent effects for low and physiologically relevant osmolyte concentrations.
Mesoscopic Simulations of Polyelectrolyte Electrophoresis in Nanochannels
[chapter]
2011
High Performance Computing in Science and Engineering '10
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We present the results of mesoscopic dissipative particle dynamics (DPD) simulations of coupled electrohydrodynamic phenomena on the micro-and nanoscale. The effects of electroosmotic flow and slippage combined with polyelectrolyte electrophoresis are investigated in detail, taking full account of hydrodynamic and electrostatic interactions. Our numerical results are in excellent agreement with analytical calculations.
doi:10.1007/978-3-642-15748-6_5
fatcat:pxok62ixqbgpxbkwqj26hhfthi
Some Notes on the Thermodynamic Accuracy of Coarse-Grained Models
2019
Frontiers in Molecular Biosciences
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et al., 2017 Michalowsky et al., , 2018 Smiatek and Holm, 2018) . ...
., 2019; Nandy and Smiatek, 2019; Smiatek, 2019) . However, some processes take place on time and length scales, which are not accessible for atomistic MD simulations. ...
, 2014 Smiatek, , 2017 Dunn and Noid, 2015; Guenza et al., 2018; Oprzeska-Zingrebe and Smiatek, 2018a) . ...
doi:10.3389/fmolb.2019.00087
pmid:31552269
pmcid:PMC6746972
fatcat:f4u3yvlqu5go5cvcy2ivnviyt4
Conformation and Dynamics of Long-Chain End-Tethered Polymers in Microchannels
2019
Polymers
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Polyelectrolytes constitute an important group of materials, used for such different purposes as the stabilization of emulsions and suspensions or oil recovery. They are also studied and utilized in the field of microfluidics. With respect to the latter, a part of the interest in polyelectrolytes inside microchannels stems from genetic analysis, considering that deoxyribonucleic acid (DNA) molecules are polyelectrolytes. This review summarizes the single-molecule experimental and molecular
doi:10.3390/polym11030488
pmid:30960472
pmcid:PMC6473708
fatcat:5o22wcj7rjdanoayagctxpzpmm
more »
... ics simulation-based studies of end-tethered polyelectrolytes, especially addressing their relaxation dynamics and deformation characteristics under various external forces in micro-confined environments. In most of these studies, DNA is considered as a model polyelectrolyte. Apart from summarizing the results obtained in that area, the most important experimental and simulation techniques are explained.
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