Fast dynamics and high effective dimensionality of liquid fluidity.

Fluidity, the ability of liquids to flow, is the key property distinguishing liquids from solids. This fluidity is set by the mobile transit atoms moving from one quasi-equilibrium point to the next. The nature of this transit motion is unknown. Here, we show that flow-enabling transits form a dynamically distinct sub-ensemble where atoms move on average faster than the overall system, with a manifestly non-Maxwellian velocity distribution. This is in contrast to solids and gases where no distinction of different ensembles can be made and where the distribution is always Maxwellian. The non-Maxwellian distribution is described by an exponent [Formula: see text] corresponding to high dimensionality of space. This is generally similar to extra synthetic dimensions in topological quantum matter, albeit higher dimensionality in liquids is not integer but is fractional. The dimensionality is close to 4 at melting and exceeds 4 at high temperature. [Formula: see text] has a maximum as a function of temperature and pressure in liquid and supercritical states, returning to its Maxwell value in the solid and gas states.

Phase behaviour of coarse-grained fluids.

Soft condensed matter structures often challenge us with complex many-body phenomena governed by collective modes spanning wide spatial and temporal domains. In order to successfully tackle such problems, mesoscopic coarse-grained (CG) statistical models are being developed, providing a dramatic reduction in computational complexity. CG models provide an intermediate step in the complex statistical framework of linking the thermodynamics of condensed phases with the properties of their constituent atoms and molecules. These allow us to offload part of the problem to the CG model itself and reformulate the remainder in terms of reduced CG phase space. However, such exchange of pawns to chess pieces, or 'Hamiltonian renormalization', is a radical step and the thermodynamics of the primary atomic and CG models could be quite distinct. Here, we present a comprehensive study of the phase diagram including binodal and interfacial properties of a dissipative particle dynamics (DPD) model, extended to include finite-range attraction to support the liquid-gas equilibrium. Despite the similarities with the atomic model potentials, its phase envelope is markedly different featuring several anomalies such as an unusually broad liquid range, change in concavity of the liquid coexistence branch with variation of the model parameters, volume contraction on fusion, temperature of maximum density in the liquid phase and negative thermal expansion in the solid phase. These results provide new insight into the connection between simple potential models and complex emergent condensed matter phenomena.

Evolution of amorphous structure under irradiation: zircon case study.

The nature of the amorphous state has been notably difficult to ascertain at the microscopic level. In addition to the fundamental importance of understanding the amorphous state, potential changes to amorphous structures as a result of radiation damage have direct implications for the pressing problem of nuclear waste encapsulation. Here, we develop new methods to identify and quantify the damage produced by high-energy collision cascades that are applicable to amorphous structures and perform large-scale molecular dynamics simulations of high-energy collision cascades in a model zircon system. We find that, whereas the averaged probes of order such as pair distribution function do not indicate structural changes, local coordination analysis shows that the amorphous structure substantially evolves due to radiation damage. Our analysis shows a correlation between the local structural changes and enthalpy. Important implications for the long-term storage of nuclear waste follow from our detection of significant local density inhomogeneities. Although we do not reach the point of convergence where the changes of the amorphous structure saturate, our results imply that the nature of this new converged amorphous state will be of substantial interest in future experimental and modeling work.

Electronic effects in high-energy radiation damage in tungsten.

Although the effects of the electronic excitations during high-energy radiation damage processes are not currently understood, it is shown that their role in the interaction of radiation with matter is important. We perform molecular dynamics simulations of high-energy collision cascades in bcc-tungsten using the coupled two-temperature molecular dynamics (2T-MD) model that incorporates both the effects of electronic stopping and electron-phonon interaction. We compare the combination of these effects on the induced damage with only the effect of electronic stopping, and conclude in several novel insights. In the 2T-MD model, the electron-phonon coupling results in less damage production in the molten region and in faster relaxation of the damage at short times. These two effects lead to a significantly smaller amount of the final damage at longer times.

Arbitrary order permanent Cartesian multipolar electrostatic interactions.

Recently, there has been a concerted effort to implement advanced classical potential energy surfaces by adding higher order multipoles to fixed point charge electrostatics in a bid to increase the accuracy of simulations of condensed phase systems. One major hurdle is the unwieldy nature of the expressions which in part has limited developers mostly to including only dipoles and quadrupoles. In this paper, we present a generalization of the Cartesian formulation of electrostatic multipolar interactions that enables the specification of an arbitrary order of multipoles. Specifically, we derive formulas for arbitrary order implementation of the particle mesh Ewald method and give a closed form formula for the stress tensor in the reciprocal space. In addition, we provide recurrence relations for common electrostatic potentials employed in molecular simulations, which allows for the generalization to arbitrary order and guarantees a computational cost that scales as O(p(3)) for Cartesian multipole interactions of order p.

Electronic effects in high-energy radiation damage in iron.

Electronic effects have been shown to be important in high-energy radiation damage processes where a high electronic temperature is expected, yet their effects are not currently understood. Here, we perform molecular dynamics simulations of high-energy collision cascades in α-iron using a coupled two-temperature molecular dynamics (2T-MD) model that incorporates both the effects of electronic stopping and electron-phonon interaction. We subsequently compare it with the model employing electronic stopping only, and find several interesting novel insights. The 2T-MD results in both decreased damage production in the thermal spike and faster relaxation of the damage at short times. Notably, the 2T-MD model gives a similar amount of final damage at longer times, which we interpret to be the result of two competing effects: a smaller amount of short-time damage and a shorter time available for damage recovery.

The nature of high-energy radiation damage in iron.

Understanding and predicting a material's performance in response to high-energy radiation damage, as well as designing future materials to be used in intense radiation environments, requires knowledge of the structure, morphology and amount of radiation-induced structural changes. We report the results of molecular dynamics simulations of high-energy radiation damage in iron in the range 0.2-0.5 MeV. We analyze and quantify the nature of collision cascades both at the global and the local scale. We observe three distinct types of damage production and relaxation, including reversible deformation around the cascade due to elastic expansion, irreversible structural damage due to ballistic displacements and smaller reversible deformation due to the shock wave. We find that the structure of high-energy collision cascades becomes increasingly continuous as opposed to showing sub-cascade branching as reported previously. At the local length scale, we find large defect clusters and novel small vacancy and interstitial clusters. These features form the basis for physical models aimed at understanding the effects of high-energy radiation damage in structural materials.

Effect of Fermi surface nesting on resonant spin excitations in Ba(1-x)K(x)Fe2As2.

We report inelastic neutron scattering measurements of the resonant spin excitations in Ba(1-x)K(x)Fe(2)As(2) over a broad range of electron band filling. The fall in the superconducting transition temperature with hole doping coincides with the magnetic excitations splitting into two incommensurate peaks because of the growing mismatch in the hole and electron Fermi surface volumes, as confirmed by a tight-binding model with s(±)-symmetry pairing. The reduction in Fermi surface nesting is accompanied by a collapse of the resonance binding energy and its spectral weight, caused by the weakening of electron-electron correlations.

[The most important stages of the mechanism of action in vivo of carcinogen diethylnitrosoamine and its effect on the synthesis of RNA, proteins, DNA, and deoxyribonucleotides].

The mechanisms of nitric oxide (NO) generation from exogenous and endogenous sources, induced by the addition of the carcinogen diethylnitrosoamine (DENA) to rat organism have been studied. Within 15 h after the addition of DENA, the carcinogen itselt acts as an exogenous NO donor. The products of protein degradation (the process induced by DENA) act as endogenous donors of NO. It was shown that the generation of nitric oxide from diethylnitrosoamine leads to deep hemic and tissue hypoxia and induces the inactivation of oxygen-dependent enzymes, including ribonucleotide reductase, and the inhibition of ATP synthesis. Under these conditions, the protein synthesis and as a consequence the synthesis of deoxyribonucleotides and DNA are strongly suppressed; i.e., diethylnitrosoamine produces the effect similar to the action of the antibiotic cycloheximide, an inhibitor of translation. The administration of cycloheximide to the animal organism also led to the appearance of a considerable amount of nitric oxide in the blood. It is assumed that nitric oxide initiates (on the administration of the carcinogen) or at least enhances (on the administration of cycloheximide) the blockage of the synthesis of the protein, deoxyribonucleotides, and DNA. In response to the disturbance of protein synthesis, the complex of enzymes is activated that accomplish the utilization of the degradation products of proteins, including the inducible form of NO synthase.

mRNA of the pro-apoptotic gene BBC3 serves as a molecular marker for TNF-α-induced islet damage in humans.

AIMS/HYPOTHESIS: TNF-α plays important roles in the pathogenesis of type 1 and type 2 diabetes mellitus. In light of this, we examined the involvement of a pro-apoptotic gene, BBC3 (also known as PUMA), in TNF-α-mediated beta cell dysfunction and destruction in human islets. METHODS: Human islets were exposed in vitro to TNF-α alone or in combination with IFN-γ. Gene expression was assessed by RT-PCR using a set of single islets. Protein abundance and cellular localisation of BBC3 were assessed by immunoblot and immunohistochemistry. A marginal number of islets were transplanted into diabetic NODscid mice to correlate in vivo islet function with BBC3 expression. RESULTS: BBC3 and IL8 mRNA were upregulated in TNF-α-stimulated islets in a dose-dependent manner and enhanced through addition of IFN-γ, but not upregulated by IFN-γ alone. Immunohistochemistry revealed that TNF-α in combination with IFN-γ upregulated basal BBC3 abundance in the cytoplasm of beta cells along with the perinuclear clustering of mitochondria partially co-localised with BBC3. TNF-α alone did not induce beta cell death, but did abrogate preproinsulin precursor mRNA synthesis in response to high glucose stimulation, which was inversely associated with upregulation of BBC3 mRNA expression by TNF-α. Higher BBC3 mRNA expression in islets correlated with decreased graft function in vivo. CONCLUSIONS/INTERPRETATION: These results suggest that BBC3 mRNA can serve as a molecular marker to detect early TNF-α-induced beta cell stress and may help identify islet-protective compounds for the treatment of diabetes.

Multifactorial nature of high frequency of mitochondrial DNA mutations in somatic mammalian cells.

The high frequency of mitochondrial DNA (mtDNA) mutations in somatic mammalian cells, which is more than two orders of magnitude higher than the mutation frequency of nuclear DNA (nDNA), significantly correlates with development of a variety of mitochondrial diseases (neurodegenerative diseases, cardiomyopathies, type II diabetes mellitus, cancer, etc.). A direct cause-consequence relationship has been established between mtDNA mutations and aging phenotypes in mammals. However, the unclear nature of the high frequency of mtDNA mutations requires a comprehensive consideration of factors that contribute to this phenomenon: oxidative stress, features of structural organization and repair of the mitochondrial genome, ribonucleotide reductase activity, replication errors, mutations of nuclear genes encoding mitochondrial proteins.

[The use of EPR spectroscopy to control the changes in organism radioresistance. Experimental results].

The responses of deoxyribonucleotide (dNTP), DNA, and protein synthesis systems in blood-forming organs of animals (dogs, mice) as well as changes in Fe(3+)-transferrin (Fe(3+)-TF) and Cu(2+)-ceruloplasmin (Cu(2+)-CP) pools in blood to gamma-irradiation and the administration of radioprotectors have been studied. It has been shown that changes in Fe(3+)-TF and Cu(2+)-CP pools in blood are indices of changes of body radioresistance and are reliably controlled by the EPR technique. An increase in the Fe(3+)-TF pool promotes the activation of synthesis of dNTP, DNA, and Fe(3+)-containing proteins, which are essential for repair efficiency during early post-irradiation time as well as for the development of compensatory and restorative reactions of cellular systems; i.e., they are responsible for body resistance to DNA-damaging factors. It is important that the intensity of responses depends on the initial state of the organism. Thus, dogs with initial individual characteristics of blood typical for "suppressed" or "activated" states had abnormally high responses to irradiation by low doses of 0.25 and 0.5 Gy. This fact is important for the estimation of consequences of prolonged low-dose irradiation for human population. It has been shown that radioprotectors, efficient in survival test activate the synthesis of dNTP, DNA, and proteins in organs. The intensity of dNTP synthesis and the time when dNTP pools get maximum values determine the efficiency of protectors and the time of irradiation after their administration.

eScience for molecular-scale simulations and the eMinerals project.

We review the work carried out within the eMinerals project to develop eScience solutions that facilitate a new generation of molecular-scale simulation work. Technological developments include integration of compute and data systems, developing of collaborative frameworks and new researcher-friendly tools for grid job submission, XML data representation, information delivery, metadata harvesting and metadata management. A number of diverse science applications will illustrate how these tools are being used for large parameter-sweep studies, an emerging type of study for which the integration of computing, data and collaboration is essential.

Unconventional superconductivity in Ba(0.6)K(0.4)Fe2As2 from inelastic neutron scattering.

A new family of superconductors containing layers of iron arsenide has attracted considerable interest because of their high transition temperatures (T(c)), some of which are >50 K, and because of similarities with the high-T(c) copper oxide superconductors. In both the iron arsenides and the copper oxides, superconductivity arises when an antiferromagnetically ordered phase has been suppressed by chemical doping. A universal feature of the copper oxide superconductors is the existence of a resonant magnetic excitation, localized in both energy and wavevector, within the superconducting phase. This resonance, which has also been observed in several heavy-fermion superconductors, is predicted to occur when the sign of the superconducting energy gap takes opposite values on different parts of the Fermi surface, an unusual gap symmetry which implies that the electron pairing interaction is repulsive at short range. Angle-resolved photoelectron spectroscopy shows no evidence of gap anisotropy in the iron arsenides, but such measurements are insensitive to the phase of the gap on separate parts of the Fermi surface. Here we report inelastic neutron scattering observations of a magnetic resonance below T(c) in Ba(0.6)K(0.4)Fe(2)As(2), a phase-sensitive measurement demonstrating that the superconducting energy gap has unconventional symmetry in the iron arsenide superconductors.

The advantages of the application of amnion membrane in the treatment of burns.

A crucial and important factor for successful treatment of burns is the early covering of the burned area with skin substitutes. The covering of the burn requires material that restores the epidermal function and integrates itself into the process of healing. Biological dressings are the golden standard for the temporary covering of burns. All biological skin substitutes are susceptible to early graft reaction and the only exception is the amnion membrane. The importance of the amnion membrane as a biological dressing for burns amounts to: a barrier to bacterial colonization, hastens the epithelisation, and control of water loss. Amnioplasty is a method of application of amnion membrane on the recipient site. In this comparative study, 60 patients with dermal and sub-dermal burns were included. Research was made on an examination group of 30 patients with burns where the method of amnioplasty was applied, and for this amnion membrane conserved in 76% alcohol was used. The control group was made up of 30 patients with burns treated conventionally, and standard methods for the local treatment of burns were applied: exposition, occlusive dressing and initial excision with skin grafting. Pathohistological and microbiological analyses of the bioptical material were made. The degree of the burns was determined through a pathohistological analysis of the bioptical material taken the third day, and in some of the subjects where re-epithelialization was determined on the seventh day, the further re-epithelialization was observed clinically. Pathohistological examination enabled discrimination between bacterial colonization and the invasive bacterial infection. Furthermore, the type of bacterial colonization and infection was determined, which was confirmed with microbiological analysis. The analysis of the results from the microbiological and pathohistological researches of the bioptical material according to the bacterial colonization and infection showed that, although between the examined and the control group there was no statistically important difference, the value of p = 0.067 is close to the statistically important value of p < 0.05. The results of the pathohistological examination of the bioptical material taken the seventh day and analysed according to the re-epithelialization showed that there was a significant difference between the two groups of p < 0.035. It should be mentioned that, although according to the microbiological examinations of the bioptical material a statistically significant difference was not achieved, clinical significance was achieved. The obtained significance of p < 0.035 compared to the re-epithelialization in both groups approved the application of the method of amnioplasty. The histological analysis of the bioptical material not only determines the degree of the burns specifically, but facilitates the choice of method for further treatment, observes the speed of the re-epithelialization and plays an important part in the correct diagnosis and the early start of the specific therapy, important in preventing sepsis. The application of amnion membrane as a biological dressing speeds the re-epithelialization and prevents invasive bacterial infection. Pathohistological examination of the burns is recommended to be established as a standard method in clinical practice.

Testing combinations of protease inhibitor and preservation solution to improve islet quality and yield.

UNLABELLED: Pancreas preservation using an oxygenated two-layer method (TLM) has been reported to improve islet yields, as has supplementation of Liberase with Pefabloc. We hypothesized that using both TLM and Pefabloc could enhance islet yield as compared with preservation in University of Wisconsin (UW) or Histidine-Tryptophan Ketoglutarate (HTK) solution. METHODS: Ninety-eight pancreata with no significant differences of age, body mass index, or cold ischemia time preserved randomly with UW (n = 40), TLM (n = 48), or HTK (n = 10) were processed with (n = 36) or without (n = 66) Pefabloc. RESULTS: The total islet equivalent (IEQ) from TLM-preserved pancreata processed with Pefabloc (n = 12) showed lower yields versus those processed without Pefabloc (n = 36): 216,120 +/- 27,906 vs. 301,427 +/- 21,447 IEQ (P < .05). Islets from 1 of 12 (8.33%) pancreata processed with Pefabloc in TLM were transplanted, in contrast with 15/36 TLM (41.67%) pancreata processed without it. Islet yields were not significantly different among pancreata preserved in UW and processed with Pefabloc (n = 17) versus without Pefabloc (n = 23): 342,693 +/- 45,588 versus 266,609 +/- 29,006 IEQ (P = .149). The number of transplants from UW-preserved pancreata was 3/17 (17.65%) when processed with Pefabloc and 4/23 (17.39%) without. Among the HTK group, there was no significant difference in islet yields between pancreata processed with (n = 7) versus without Pefabloc (n = 3): 248,227 +/- 65,294 versus 483,555 +/- 144,070 IEQ (P = .118). CONCLUSIONS: Pefabloc showed no benefit to improve islet yields. Pancreata preserved in TLM provided better transplant quality islets when processed in the absence of Pefabloc.

Glucose-stimulated increment in oxygen consumption rate as a standardized test of human islet quality.

Standardized assessment of islet quality is imperative for clinical islet transplantation. We have previously shown that the increment in oxygen consumption rate stimulated by glucose (DeltaOCR(glc)) can predict in vivo efficacy of islet transplantation in mice. To further evaluate the approach, we studied three factors: islet specificity, islet composition and agreement between results obtained by different groups. Equivalent perifusion systems were set up at the City of Hope and the University of Washington and the values of DeltaOCR(glc) obtained at both institutions were compared. Islet specificity was determined by comparing DeltaOCR(glc) in islet and nonislet tissue. The DeltaOCR(glc) ranged from 0.01 to 0.19 nmol/min/100 islets (n = 14), a wide range in islet quality, but the values obtained by the two centers were similar. The contribution from nonislet impurities was negligible (DeltaOCR(glc) was 0.12 nmol/min/100 islets vs. 0.007 nmol/min/100 nonislet clusters). The DeltaOCR(glc) was statistically independent of percent beta cells, demonstrating that DeltaOCR(glc) is governed more by islet quality than by islet composition. The DeltaOCR(glc), but not the absolute level of OCR, was predictive of reversal of hyperglycemia in diabetic mice. These demonstrations lay the foundation for testing DeltaOCR(glc) as a measurement of islet quality for human islet transplantation.

Improvement of human islet cryopreservation by a p38 MAPK inhibitor.

The activation of p38 mitogen-activated protein kinase (MAPK) has been shown to cause ischemia/reperfusion injury of several organs used for transplantation and also to play a significant role in primary islet graft nonfunction. Activation of p38 MAPK may also occur during islet cryopreservation and thawing. In this study, a p38 MAPK inhibitor (p38IH) was applied to human islet cryopreservation to improve islet yield and quality after thawing. Under serum-free conditions, human islets were cryopreserved, thawed and cultured using our standard procedures. Three types of solutions were tested: conventional RPMI1640 medium (RPMI), a newly developed islet cryopreservation solution (ICS), and ICS supplemented with a p38IH, SD-282 (ICS-p38IH). Activation or inhibition of p38 MAPK was demonstrated by the diminished phosphorylation of HSP27 substrate. Islet recovery on day 2 after thawing was highest with ICS-p38IH and islet viability was not significantly different in the three groups. beta Cell numbers and function were the highest in islets cryopreserved with ICS-p38IH. Glucose-stimulated human C-peptide levels were 86% of that of the nonfrozen islets when measured 4 weeks after transplantation into NODscid mice. This improvement may provide an opportunity to establish islet banks and allow the use of cryopreserved islets for clinical transplantation.

Mesenchymal stem cells facilitate the induction of mixed hematopoietic chimerism and islet allograft tolerance without GVHD in the rat.

Induction of hematopoietic chimerism and subsequent donor-specific immune tolerance via bone marrow transplantation is an ideal approach for islet transplantation to treat type-1 diabetes. We examined the potential of mesenchymal stem cells (MSCs) in the induction of chimerism and islet allograft tolerance without the incidence of graft-versus-host disease (GVHD). Streptozotocin-diabetic rats received a conditioning regimen consisting of antilymphocyte serum and 5 Gy total body irradiation, followed by an intraportal co-infusion of allogeneic MSCs, bone marrow cells (BMCs) and islets. Although all the recipients rejected the islets initially, half of them developed stable mixed chimerism and donor-specific immune tolerance, shown by the engraftment of donor skin and second-set islet transplants and acute rejection of a third-party skin. The engraftment of the primary islet allografts with stable chimerism was achieved by the addition of a 2-week peritransplant administration of 15-deoxyspergualin (DSG). Without MSCs, none of the recipients treated with DSG developed chimerism or reversal of diabetes. GVHD was not observed in any of the recipients infused with MSCs (0/15), whereas it occurred in 4/11 recipients without MSCs. These results indicate a potential use of MSCs for induction of hematopoietic chimerism and subsequent immune tolerance in clinical islet transplantation.

[The inhibitor of free radical processes decrease of protein biosynthesis in gun short wound tissues and weaken development of the general adaptation syndrome].

The dynamics of total protein biosynthesis and procollagen biosynthesis in skeletal muscle of injury tissues with the antioxidant BHT (dibunol) treatment and with common healing were studied. The obtained date indicate that the AO treatment reduce the rate of biosynthesis both the total proteins and procollagen at the 3th day of healing. Dibunol also considerably reduce the protein biosynthesis in adrenals and brake of corticosteroids biogenesis as measured by ESR-signals intensity of reduced adrenodoxine. AO treatment also reduce the protein biosynthesis in thymus, spleen and bone marrow. The lowering of functional activity of endocrine and immune systems indicate that the AO significantly inhibit the systemic reactions of organism induced by acute wound affect. It was suggested that as "primary mediator" of stress-reaction may be considered lipoperoxide radicals and decay products of lipohydroperoide.