Poisson-Boltzmann Theory of Charged Colloids: Limits of the Cell Model for Salty Suspensions

Thermodynamic properties of charge-stabilised colloidal suspensions are commonly modeled by implementing the mean-field Poisson-Boltzmann (PB) theory within a cell model. This approach models a bulk system by a single macroion, together with counterions and salt ions, confined to a symmetrically shaped, electroneutral cell. While easing solution of the nonlinear PB equation, the cell model neglects microion-induced correlations between macroions, precluding modeling of macroion ordering phenomena. An alternative approach, avoiding artificial constraints of cell geometry, maps a macroion-microion mixture onto a one-component model of pseudo-macroions governed by effective interactions. In practice, effective-interaction models are usually based on linear screening approximations, which can accurately describe nonlinear screening only by incorporating an effective (renormalized) macroion charge. Combining charge renormalization and linearized PB theories, in both the cell model and an effective-interaction (cell-free) model, we compute osmotic pressures of highly charged colloids and monovalent microions over a range of concentrations. By comparing predictions with primitive model simulation data for salt-free suspensions, and with predictions of nonlinear PB theory for salty suspensions, we chart the limits of both the cell model and linear-screening approximations in modeling bulk thermodynamic properties. Up to moderately strong electrostatic couplings, the cell model proves accurate in predicting osmotic pressures of deionized suspensions. With increasing salt concentration, however, the relative contribution of macroion interactions grows, leading predictions of the cell and effective-interaction models to deviate. No evidence is found for a liquid-vapour phase instability driven by monovalent microions. These results may guide applications of PB theory to soft materials.Comment: 27 pages, 5 figures, special issue of Journal of Physics: Condensed Matter on "Classical density functional theory methods in soft and hard matter

Challenges in molecular simulation of homogeneous ice nucleation

NoWe address the problem of recognition and growth of ice nuclei in simulation of supercooled bulk water. Bond orientation order parameters based on the spherical harmonics analysis are shown to be ineffective when applied to ice nucleation. Here we present an alternative method which robustly differentiates between hexagonal and cubic ice forms. The method is based on accumulation of the maximum projection of bond orientations onto a set of predetermined vectors, where different terms can contribute with opposite signs with the result that the irrelevant or incompatible molecular arrangements are damped out. We also introduce an effective cluster size by assigning a quality weight to each molecule in an ice-like cluster. We employ our cluster analysis in Monte Carlo simulation of homogeneous ice formation. Replica-exchange umbrella sampling is used for biasing the growth of the largest cluster and calculating the associated free energy barrier. Our results suggest that the ice formation can be seen as a two-stage process. Initially, short tetrahedrally arranged threads and rings are present; these become correlated and form a diffuse ice-genic network. Later, hydrogen bond arrangements within the amorphous ice-like structure gradually settle down and simultaneously `tune-up¿ nearby water molecules. As a result, a well-shaped ice core emerges and spreads throughout the system. The process is very slow and diverse owing to the rough energetic landscape and sluggish molecular motion in supercooled water, while large configurational fluctuations are needed for crystallization to occur. In the small systems studied so far the highly cooperative molecular rearrangements eventually lead to a relatively fast percolation of the forming ice structure through the periodic boundaries, which inevitably affects the simulation results.EPSR

Estimating thermodynamic expectations and free energies in expanded ensemble simulations systematic variance reduction through conditioning

International audienceMarkov chain Monte Carlo methods are primarily used for sampling from a given probability distribution and estimating multi-dimensional integrals based on the information contained in the generated samples. Whenever it is possible, more accurate estimates are obtained by combining Monte Carlo integration and integration by numerical quadrature along particular coordinates. We show that this variance reduction technique, referred to as conditioning in probability theory, can be advantageously implemented in -emph{expanded ensemble} simulations. These simulations aim at estimating thermodynamic expectations as a function of an external parameter that is sampled like an additional coordinate. Conditioning therein entails integrating along the external coordinate by numerical quadrature. We prove variance reduction with respect to alternative standard estimators and demonstrate the practical efficiency of the technique by estimating free energies and characterizing a structural phase transition between two solid phases

Communication: Conformation state diagram of polypeptides: A chain length induced α - β transition

By using a generic coarse grained polypeptide model, we perform multicanonical molecular dynamics simulations for determining the equilibrium conformation state diagram of a single homopolypeptide chain as a function of the chain length and temperature. The state diagram highlights the thermal regimes of stability for various conformational patterns in polypeptides, including swollen, random and collapsed coils, globular structures, extended and bended helices, and compact bundles. Remarkably, at low temperatures we observe a sharp transition from extended helix to compact bundles as the chain length increases. This finding indicates that the chain length is one of the intrisic factors that can trigger - transformations in a broad class of polypeptides. © 2011 American Institute of Physics

DL_MONTE:A multipurpose code for Monte Carlo simulation

DL_MONTE is an open source, general-purpose software package for performing Monte Carlo simulations. It includes a wide variety of force fields and MC techniques, and thus is applicable to a broad range of problems in molecular simulation. Here we provide an overview of DL_MONTE, focusing on key features recently added to the package. These include the ability to treat systems confined to a planar pore (i.e. `slit' or `slab' boundary conditions); the lattice-switch Monte Carlo (LSMC) method for evaluating precise free energy differences between competing polymorphs; various commonly-used methods for evaluating free energy profiles along transition pathways (including umbrella sampling, Wang-Landau and transition matrix); and a supplementary Python toolkit for simulation management and application of the histogram reweighting analysis method. We provide two `real world' examples to elucidate the use of these methods in DL_MONTE. In particular, we apply umbrella sampling to calculate the free energy profile associated with the translocation of a lipid through a bilayer. Moreover we employ LSMC to examine the thermodynamic stability of two plastic crystal phases of water at high pressure. Beyond this, we provide instructions on how to access DL_MONTE, and point to additional information valuable to existing and prospective users

Problems of Safety, Occupational Hygiene and Control Over Infections in Fighting with Occupational Diseases of Healthcare Workers with COVID-19 in Treatment Facilities of Ukraine

The objective of the publication was to assess the safety of treatment facilities, occupational health and infection control in Kiev, Zhytomyr and Zhytomyr region to enhance risk management of SARS-CoV-2 infection of healthcare workers and reduce occupational illness and mortality for COVID-19. Bibliosemantic, hygienic, questionnaire, statistical methods and methods of comparative and system analysis have been used. The work of doctors involved in overcoming COVID-19 pandemic is classified as dangerous (extreme). In addition to the SARS-CoV-2 virus, the working conditions of medical workers are influenced by physical, chemical factors and high physical and neuro-emotional stress. Among medical workers of the Zhytomyr region who were diagnosed with an acute occupational disease COVID-19, nurses prevailed (38.57%). Junior nurses (26.1%) – the second COVID-19 incidence, paramedics (5.31%) occupy the third place. The doctors' incidence was ranked in the following sequence: doctors of GPFM – 4.85%, surgeons – 4.16%, anesthesiologists – 2.54%, infectious disease doctors – 2.08%, radiologists – 1.85%. This distribution of medical professions is observed for all Ukraine regions. Chance of becoming infected with SARS CoV 2 for healthcare workers in October was by 3.8 times higher than the general population. Risk of dying from COVID-19 in healthcare workers is greater by 1.5 times than the general population. The high level of occupational morbidity of COVID-19 in Ukrainian medical personnel is determined by personal negligence, incomplete staffing of TF with medical workers, of medical workers with PPE; dis-use of PPE if available, absence or poor-quality instruction on labor protection; shortage of epidemiologists, hygienists and occupational pathologists

Patient Safety Culture in Health Care Facilities in Ukraine (Message 1)

Using a questionnaire from the United States Agency for Research and Quality in Health Care (AHRQ), the characteristics of patient safety (PS) culture in the staff of various health care facilities (HCF) in Ukraine were analyzed. In addition, the characteristics of PS culture were analyzed depending on the length of service and affiliation of the respondents to the medical or nursing staff, as well as the profile of therapeutic or surgical activities. It is established that the weakness of the PS culture of the staff of domestic HCF is "Reaction to mistakes" (less than 30% of positive responses), which indicates the predominance of culture of accusation (unfair culture) in Ukrainian HCF and as a consequence fears of the staff to disclose mistakes and accordingly, the lack of opportunity to learn from these mistakes.“Staffing” is identified as a weakness of the PS culture (less than 50% of positive responses) in most comparison groups. It is worth noting such a characteristic of the culture of BP, as the "Frequency of error messages" (less than 70% of positive responses). The Cronbach's alpha coefficient in all groups of respondents ranged from 0.62 to 0.78, which indicates the truth of the results of the study

A Comparative Analysis on Safety Culture in Domestic and Foreign Health Care Facilities and Enterprises of Other Activities (Message 2)

The characteristics of the safety culture of patients and personnel in health care facilities in Ukraine as a whole and separately among doctors-pathologists are analyzed with correlation of the data obtained with similar indicators of the culture of patient safety in medical facilities of other countries and comparison with the safety culture of workers of domestic nuclear power plants. It was confirmed that the weaknesses of the safety culture of the personnel of domestic hospitals is characterized by "Reaction to mistakes", which indicates the prevalence of the culture of blame (unfair culture) in domestic hospitals and, as a result, the absence of real data on medical errors and other incidents of patient safety. The high percentage of positive responses to the safety culture characteristic “Response to mistakes” among the workers of Ukrainian nuclear power plants is an example of the possibility of forming an appropriate safety culture in a separate domestic industry, and the high percentage of positive answers by this characteristic in domestic pathologists is a significant potential for the development of a safe hospital environment for patients. in Ukraine

Freezing or wrapping: the role of particle size in the mechanism of nanoparticle-biomembrane interaction.

Understanding the interactions between nanoparticles (NPs) and biological matter is a high-priority research area because of the importance of elucidating the physical mechanisms underlying the interactions leading to NP potential toxicity as well as NP viability as therapeutic vectors in nanomedicine. Here, we use two model membrane systems, giant unilamellar vesicles (GUVs) and supported monolayers, to demonstrate the competition between adhesion and elastic energy at the nanobio interface, leading to different mechanisms of NP-membrane interaction relating to NP size. Small NPs (18 nm) cause a "freeze effect" of otherwise fluid phospholipids, significantly decreasing the phospholipid lateral mobility. The release of tension through stress-induced fracture mechanics results in a single microsize hole in the GUVs after interaction. Large particles (>78 nm) promote membrane wrapping, which leads to increased lipid lateral mobility and the eventual collapse of the vesicles. Electrochemical impedance spectroscopy on the supported monolayer model confirms that differently sized NPs interact differently with the phospholipids in close proximity to the electrode during the lipid desorption process. The time scale of these processes is in accordance with the proposed NP/GUV interaction mechanism