Computing the local pressure in molecular dynamics simulations

Computer simulations of inhomogeneous soft matter systems often require accurate methods for computing the local pressure. We present a simple derivation, based on the virial relation, of two equivalent expressions for the local (atomistic) pressure in a molecular dynamics simulation. One of these expressions, previously derived by other authors via a different route, involves summation over interactions between particles within the region of interest; the other involves summation over interactions across the boundary of the region of interest. We illustrate our derivation using simulations of a simple osmotic system; both expressions produce accurate results even when the region of interest over which the pressure is measured is very small.Comment: 11 pages, 4 figure

Copper staining/labeling and scanning electrochemical microscopy readout of proteins on poly(vinylidene difluoride) membranes

Scanning Electrochemical Microscopy (SECM) is used in combination with copper labeling to visualize roteins on surfaces. Proteins are adsorbed on a poly(vinylidene difluoride) (PVDF) membrane and stained using a standard protocol involving copper salts. The latter are then reduced to copper metal and further detected by SECM with ferrocene methanol as a redox mediator in aqueous solution. During the SECM scan, the potential is held at a value at which the oxidation of the redox mediator occurs and a positive feedback current is detected when scanning over copper clusters. A negative feedback is observed elsewhere

Detection of proteins on membranes and in microchannels using copper staining combined with Scanning Electrochemical Microscopy

Scanning Electrochemical Microscopy (SECM) and copper staining are combined to achieve visualisation of proteins on surfaces. Proteins are adsorbed on a polyvinylidene fluoride (PVDF) membrane or on a polyethylene terephthalate (PET) surface and stained using a standard protocol involving copper salts. Salts are then reduced to copper and detected by SECM with ferrocene methanol as a redox mediator in aqueous solution. During the SECM scan, the potential is held at a value at which the oxidation of the redox mediator occurs and a positive feedback current is detected when scanning over copper clusters. A negative feedback is observed elsewhere. This method enables unspecific protein adsorption mapping on polymeric membranes and into microchannels without any requirement of enzymatic activity or affinity to a labelled secondary reporter

Capillary Electrophoresis as a Second Dimension to Isoelectric Focusing for Peptide Separation

Capillary zone electrophoresis and carrier ampholytes based capillary electrophoresis have been used as a second separation step to Off-Gel isoelectric focusing for the analysis of complex peptide mixtures. A tryptic digest of four proteins (bovine serum albumin, β-lactoglobulin, horse myoglobin, cytochrome c) has been chosen as a peptide test mixture. After assessment of different modes of capillary electrophoresis as a second dimension to Off-Gel isoelectric focusing, the optimized two-dimensional platforms provide a degree of orthogonality comparable to state-of-the-art multidimensional liquid chromatography systems as well as a practical peak capacity above 700

From symbolic constraint automata to Promela

In this paper, we study a subclass of constraint automata with local variables. The fragment denotes an executable subset of constraint automata for which synchronization and data constraints are expressed in an imperative guarded command style, instead of a denotational style as in the coordination language Reo. To demonstrate the executability property, we provide a translation scheme from symbolic constraint automata to Promela, the language of the model checker Spin. As a proof of concept, we model in Reo a software defined network circuit, and use the Spin model checker to verify that our model satisfies some temporal properties. (C) 2022 The Author(s). Published by Elsevier Inc.Algorithms and the Foundations of Software technolog

Electrokinetic supercharging for highly efficient peptide preconcentration in capillary zone electrophoresis

Electrokinetic supercharging has been integrated in CZE for the development of a highly sensitive methodology for protein tryptic digest analysis. A careful choice of the experimental conditions led to sensitivity enhancement factors between 1000 and 10 000 whilst maintaining a satisfactory resolution. Peptides in the low nanomolar concentration range have been detected despite the use of the poorly sensitive UV absorbance detection mode. The buffer system used in this study is fully suitable for coupling CE to MS

Chaplain care in pediatric oncology: Insight for interprofessional collaboration

Background Although attending to spiritual and religious needs is part of high quality care of pediatric cancer patients, oncology clinicians may not understand the role of the chaplain, resulting in underutilization of resources and failure to fully integrate the chaplain into the clinical team. We provide a description of what the chaplain does in the care of pediatric oncology patients. Methods We conducted a qualitative content analysis of chaplain chart notes over a one‐year period on the pediatric oncology service at a freestanding children's hospital. Using criteria designed to capture multiple potential factors in chaplain referral, we selected 30 patients for thematic analysis. Results In 2016, 166 pediatric patients were diagnosed with cancer and received ongoing care at our institution. From the 30 patients selected, 230 chaplain encounters were documented in the medical chart. Three major themes emerged. (1) The chaplains provided a rich description of spiritual and psychosocial aspects of the patient and family's experience; (2) chaplains provided diverse interventions, both religious and secular in nature; and (3) chaplains provided care within a longitudinal relationship. All three themes depend on the empathic listening by a chaplain. Conclusions The chaplains’ observations about patient and family beliefs, experiences, and emotional/spiritual states have the potential to inform the interdisciplinary care of the patient. Chaplain documentation provides insight into how spiritual care interventions and close relationships may promote patient and family well‐being. In future work, we will explore how to give voice to their insights in caring for pediatric oncology patients