Publications by authors named "Richard Chudoba"

The consecutive binding of two potassium ions to a bis(18-crown-6) analogue of Tröger's base (BCETB) in water was studied by isothermal titration calorimetry using four different salts, KCl, KI, KSCN, and KSO. A counterintuitive result was observed: the enthalpy change associated with the binding of the second ion is more negative than that of the first (Δ < Δ). This remarkable finding is supported by continuum electrostatic theory as well as by atomic scale replica exchange molecular dynamics simulations, where the latter robustly reproduces experimental trends for all simulated salts, KCl, KI, and KSCN, using multiple force fields.

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We study the permeability and selectivity ('permselectivity') of model membranes made of polydisperse polymer networks for molecular penetrant transport, using coarse-grained, implicit-solvent computer simulations. In our work, permeability P is determined on the linear-response level using the solution-diffusion model, P = KDin, i.e.

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The selective solute partitioning within a polymeric network is of key importance to applications in which controlled release or uptake of solutes in a responsive hydrogel is required. In this work we investigate the impact of cross-links on solute adsorption in a swollen polymer network by means of all-atom, explicit-water molecular dynamics simulations. We focus on a representative network subunit consisting of poly(N-isopropylacrylamide) (PNIPAM) and N,N'-methylenebisacrylamide (BIS/MBA) cross-linker types.

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The experimentally observed swelling and collapse response of weakly charged polymers to the addition of specific salts displays quite convoluted behavior that is not easy to categorize. Here we use a minimalistic implicit-solvent/explicit-salt simulation model with a focus on ion-specific interactions between ions and a single weakly charged polyelectrolyte to qualitatively explain the observed effects. In particular, we demonstrate ion-specific screening and bridging effects cause collapse at low salt concentrations whereas the same strong ion-specific direct interactions drive re-entrant swelling at high concentrations.

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Article Synopsis
  • The study uses molecular dynamics simulations to examine how the shape and chemical properties of small ligands affect their binding to hydrophobic sites.
  • It focuses on aromatic compounds that vary in their hydrophilic/hydrophobic characteristics, revealing that binding often leads to desolvation of hydrophobic areas.
  • Ligands with varying orientation patterns experience higher kinetic barriers for binding compared to more uniform shapes, influencing their binding and unbinding times significantly.
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A temperature (T)-dependent coarse-grained (CG) Hamiltonian of polyethylene glycol/oxide (PEG/PEO) in aqueous solution is reported to be used in implicit-solvent material models in a wide temperature (i.e., solvent quality) range.

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Thermoresponsive polymer architectures have become integral building blocks of 'smart' functional materials in modern applications. For a large range of developments, e.g.

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We study statistical copolymerization effects on the upper critical solution temperature (CST) of generic homopolymers by means of coarse-grained Langevin dynamics computer simulations and mean-field theory. Our systematic investigation reveals that the CST can change monotonically or non-monotonically with copolymerization, as observed in experimental studies, depending on the degree of non-additivity of the monomer (A-B) cross-interactions. The simulation findings are confirmed and qualitatively explained by a combination of a two-component Flory-de Gennes model for polymer collapse and a simple thermodynamic expansion approach.

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A new method for the determination of nitrite and nitrate, indicators of various neurological diseases (meningitis, multiple sclerosis, Parkinson's disease) in cerebrospinal fluid (CSF) on an electrophoresis chip was developed. An on-line combination of isotachophoresis (ITP) with capillary electrophoresis (CE) on a poly(methylmethacrylate) chip assembled with coupled separation channels (CC) and contact conductivity detectors was employed. ITP separations performed at low pH (3.

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There is a growing interest in evaluating molecular markers as predictors of response to new generation of targeted cancer therapies. One of such areas is biological therapy targeting epidermal growth factor receptor gene (EGFR) in lung cancer. The testing of tumor tissue is focused on specific EGFR mutations and EGFR gene amplification, since tumors exhibiting positivity of either of the two marker types are highly sensitive towards the treatment.

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System peaks are important but often also disturbing phenomena occurring in separation systems. Behavior of system peaks was studied in reversed phase high performance liquid chromatography (RP HPLC) systems consisting of an RP Amide C16 column and aqueous solutions of organic acids with alkaline metal hydroxides as mobile phases. Binary mobile phases, composed of benzoic acid and lithium hydroxide (LiOH) or cesium hydroxide (CsOH), yielded two system peaks.

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