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We present a C++ class library for Monte Carlo simulation of molecular systems, including proteins in solution. The design is generic and highly modular, enabling multiple developers to easily implement additional features. The statistical mechanical methods are documented by extensive use of code comments that – subsequently – are collected to(More)
Clonazepam (CNP) and its principal metabolite in plasma, 7-amino-CNP (ACNP), have been investigated in a prospective study of 27 newly diagnosed epileptics and correlated with specified side-effects. At a daily dose of 6 mg, the average plasma levels of both substances were about 50ng/ml, and individual values ranged from 30 to about 80ng/ml. There was a(More)
BACKGROUND One-lung ventilation (OLV) during thoracoabdominal esophagectomy may induce an inflammatory response that can contribute to the induction and propagation of frequently occurring postoperative respiratory distress. Markers of such a response might be detected in the pulmonary as well as in the systemic circulation. Inflammation and tissue damage(More)
Using molecular dynamics simulations in an explicit aqueous solvent, we examine the binding of fluoride versus iodide to a spherical macromolecule with both hydrophobic and positively charged patches. Rationalizing our observations, we divide the ion association interaction into two mechanisms: (1) poorly solvated iodide ions are attracted to hydrophobic(More)
BACKGROUND Neoadjuvant therapy for cancer of the esophagus or gastroesophageal (GE)-junction is well established. The pros and cons of chemoradiotherapy and chemotherapy are debated. Chemoradiotherapy might impair cardiac function eliciting postoperative morbidity. The aim of this pilot study was to describe acute changes in left ventricular function(More)
Large anions are attracted to hydrophobic surfaces while smaller, well solvated ions are repelled. Using a combination of explicit solvent and continuum model simulations we show that this leads to significant ion-specific protein-protein interactions due to hydrophobic patches on the protein surfaces. In solutions of NaI and NaCl we calculate the(More)
Pairing of halide anions with ammonium, as well as with trialkylated and tetraalkylated ammonium cations in water, is investigated by molecular dynamics simulations, which are verified by ab initio calculations and experimental excess chemical potentials. We find that ammonium prefers to pair with smaller halides over the larger ones, while the order is(More)
The behavior of guanidinium chloride at the surface of aqueous solutions is investigated using classical molecular dynamics (MD) simulations. It is found that the population of guanidinium ions oriented parallel to the interface is greater in the surface region than in bulk. The opposite is true for ions in other orientations. Overall, guanidinium chloride(More)
Oblivious to ion specificity, pH has been a key parameter for macromolecular solutions for little more than a century. We here widen the concept by describing the ionization of macromolecules not only via pH, but also pX where X are other binding species. Using binding constants, measured by NMR, of chloride and thiocyanate to amino acid motifs on(More)
It is known that the overall charge of a protein can change as the molecule approaches a charged object like another protein or a cell membrane. We have formalized this mechanism using a statistical mechanical framework and show how this rather overlooked interaction increases the attraction between protein molecules. From the theory, we can identify a(More)