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.

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.

Increased expression of cyclooxygenase-2 in human pancreatic islets treated with high glucose or ligands of the advanced glycation endproduct-specific receptor (AGER), and in islets from diabetic mice.

AIMS/HYPOTHESIS: The cyclooxygenase-2 (PTGS2, previously known as COX2) enzyme and its products, such as prostaglandin E(2) (PGE(2)), have been implicated in the pathogenesis of several inflammatory diseases including islet dysfunction under diabetic conditions. In this study we evaluated whether diabetic conditions in vitro, such as high-glucose (HG) culture or AGE, or in vivo in animal models of diabetes can induce PTGS2 expression and activity in pancreatic islets. MATERIALS AND METHODS: Isolated human pancreatic islets were treated for 24 h with HG (25 mmol/l) or with S100b (5 mg/l), a specific ligand for the AGE-specific receptor. PTGS2 and cyclooxygenase-1 (PTGS1, previously known as COX1) mRNA, protein expression and product PGE(2) were analysed by RT-PCR, Western blots and specific enzyme immunoassay respectively. Islet PTGS2 production in animal models was assessed by immunofluorescence. RESULTS: Treatment of human pancreatic islets with HG and S100b led to a three-five-fold induction of PTGS2 mRNA (p<0.001). PTGS2 protein and its product PGE(2) (351.4+/-13.05 fg/ml vs control 39.4+/-0.11 fg/ml) were also increased (p<0.001). Pretreatment with specific inhibitors demonstrated the involvement of protein kinase C and oxidant stress in S100b- and HG-induced PTGS2 expression. However, insulin secretion was not significantly altered by S100b. Double immunofluorescent staining showed increased PTGS2 production in pancreatic islets from diabetic mice relative to corresponding controls. CONCLUSION/INTERPRETATION: These results show for the first time that diabetes as well as diabetic conditions such as AGE and HG in vitro can directly upregulate the expression of the inflammatory PTGS2 gene in pancreatic islets. This might contribute to the pathogenesis of islet dysfunction in diabetes.

DL_POLY_3: the CCP5 national UK code for molecular-dynamics simulations.

DL_POLY_3 is a general-purpose molecular-dynamics simulation package embedding a highly efficient domain decomposition (DD) parallelization strategy. It was developed at Daresbury Laboratory under the auspices of the Engineering and Physical Sciences Research Council. Written to support academic research, it has a wide range of applications and will run on a wide range of computers; from single-processor workstations to multi-processor computers, with accent on the efficient use of multi-processor power. A new DD adaptation of the smoothed particle mesh Ewald method for calculating long-range forces in molecular simulations, incorporating a novel three-dimensional fast Fourier transform (the Daresbury Advanced Fourier Transform), makes it possible to simulate systems of the order of one million particles and beyond. DL_POLY_3 structure, functionality, performance and availability are described in this feature paper.

MCM2 is an independent predictor of survival in patients with non-small-cell lung cancer.

PURPOSE: Minichromosome maintenance protein 2 (MCM2) is a component of the prereplicative complex. It is essential for eukaryotic DNA replication and is only expressed in proliferating cells. The prognostic utility of MCM2 compared with Ki-67, another marker of proliferating cells, on survival of patients with non-small-cell lung cancer (NSCLC) was studied. PATIENTS AND METHODS: We examined the immunohistochemical expression of MCM2 and Ki-67 in primary pathologic tumor specimens from 221 NSCLC patients. For each marker, the fraction of tumor cells with positive staining was assessed as a percentage and categorized into four groups: 0% to 24%, 25% to 49%, 50% to 74%, and > or = 75%. MCM2 and Ki-67 immunoreactivities were compared with each other, and associations with pathologic and clinical parameters predictive of survival were analyzed with the chi(2) test. Cox regression models were used to assess associations between MCM2 and Ki-67 and survival while controlling for confounders. RESULTS: Independent variables significantly associated with survival were tumor stage, performance status, and staining category. Patients with less than 25% MCM2 immunoreactivity had a longer median survival time than patients with > or = 25% MCM2 immunoreactivity (46 v 31 months; P =.039) and a lower relative risk (RR) of death (RR, 0.55, 95% confidence interval, 0.34 to 0.88). There was no significant association between survival and Ki-67 expression. CONCLUSION: Immunostaining of tumor cells for MCM2 is an independent prognostic parameter of survival for patients with NSCLC. Interpretable results can be obtained on more than 96% of paraffin-embedded specimens, and approximately 35% will be in the favorable subgroup, with less than 25% positively stained tumor cells. Whether MCM2 is predictive of response to therapy needs to be studied.

MCM2--a promising marker for premalignant lesions of the lung: a cohort study.

BACKGROUND: Because cells progressing to cancer must proliferate, marker proteins specific to proliferating cells may permit detection of premalignant lesions. Here we compared the sensitivities of a classic proliferation marker, Ki-67, with a new proliferation marker, MCM2, in 41 bronchial biopsy specimens representing normal mucosa, metaplasia, dysplasia, and carcinoma in situ. METHODS: Parallel sections were stained with antibodies against MCM2 and Ki-67, and the frequencies of staining were independently measured by two investigators. Differences were evaluated statistically using the two-sided correlated samples t-test and Wilcoxon rank sum test. RESULTS: For each of the 41 specimens, the average frequency of staining by anti-MCM2 (39%) was significantly (p < 0.001) greater than by anti-Ki-67 (16%). In metaplastic lesions anti-MCM2 frequently detected cells near the epithelial surface, while anti-Ki-67 did not. CONCLUSIONS: We conclude that MCM2 is detectable in 2-3 times more proliferating premalignant lung cells than is Ki-67. The promise of MCM2 as a sensitive marker for premalignant lung cells is enhanced by the fact that it is present in cells at the surface of metaplastic lung lesions, which are more likely to be exfoliated into sputum. Future studies will determine if use of anti-MCM2 makes possible sufficiently early detection to significantly enhance lung cancer survival rates.

A factor analysis of dyspnea indexes and lung function parameters in patients with chronic obstructive pulmonary disease.

The purpose of the present study was to investigate the correlation between dyspnea ratings and a large group of lung function parameters, and extract those factors that best reflect the functional profile of patients with COPD using factor analysis. Ninety nine patients with COPD in stable clinical condition (age 60 +/- 8 years, ATS score = 2.5 +/- 0.9, FEV1% pred. = 33 +/- 13%) were included in the study. The factor analysis of the results yielded 5 factors which accounted for 80.1% of the total variance of the changes. The highest coefficients found between the factors and the original group of variables after Varimax rotation are given in the following table: Factor 1: Oxygen-cost diagram: 0.92; ATS dyspnea score: -0.80; TL,CO/VA: 0.78; Factor 2: FEV1% pred.: 0.87; FEV1/VC%: 0.86; FEV1L: 0.79; Factor 3: MIF50% pred.: 0.85; FIV1% pred.: 0.76; PImax: 0.67; Factor 4: PaCO2: -0.81; SaO2: 0.77; Mean pulmonary arterial pressure: -0.67 Factor 5: Age: 0.88; Six minutes walk distance: -0.72 The factor analysis showed that the functional profile of COPD patients has several dimensions. Therefore, in order to have COPD comprehensively evaluated, assessment of dyspnea and the respective set of lung function parameters (exercise capacity, forced inspiration and pulmonary hemodynamics), should be included in the battery of tests, besides the conventional tests.

The replication capacity of intact mammalian nuclei in Xenopus egg extracts declines with quiescence, but the residual DNA synthesis is independent of Xenopus MCM proteins.

In eukaryotes, the initiation of DNA synthesis requires the assembly of a pre-replicative complex (pre-RC) at origins of replication. This involves the sequential binding of ORC (origin-recognition-complex), Cdc6 and MCM proteins, a process referred to as licensing. After origin firing, the Cdc6 and MCM proteins dissociate from the chromatin, and do not rebind until after the completion of mitosis, thereby restricting replication to a single round in each cell cycle. Although nuclei normally become licensed for replication as they enter G(1), the extent to which the license is retained when cells enter the quiescent state (G(0)) is controversial. Here we show that the replication capacity of nuclei from Swiss 3T3 cells, in Xenopus egg extracts, is not lost abruptly with the onset of quiescence, but instead declines gradually. The decline in replication capacity, which affects both the number of nuclei induced to replicate and their subsequent rate of DNA synthesis, is accompanied by a fall in the level of chromatin-bound MCM2. When quiescent nuclei are incubated in egg extracts, they do not bind further MCMs unless the nuclei are first permeabilized. The residual replication capacity of intact nuclei must therefore be dependent on the remaining endogenous MCMs. Although high levels of Cdk activity are known to block MCM binding, we show that the failure of intact nuclei in egg extracts to increase their bound MCMs is not due to their uptake and accumulation of Cdk complexes. Instead, the failure of binding must be due to exclusion of some other binding factor from the nucleus, or to the presence within nuclei of an inhibitor of binding other than Cdk activity. In contrast to the situation in Xenopus egg extracts, following serum stimulation of intact quiescent cells, the level of bound MCMs does increase before the cells reach S phase, without any disruption of the nuclear envelope.

Mcm2, but not RPA, is a component of the mammalian early G1-phase prereplication complex.

Previous experiments in Xenopus egg extracts identified what appeared to be two independently assembled prereplication complexes (pre-RCs) for DNA replication: the stepwise assembly of ORC, Cdc6, and Mcm onto chromatin, and the FFA-1-mediated recruitment of RPA into foci on chromatin. We have investigated whether both of these pre-RCs can be detected in Chinese hamster ovary (CHO) cells. Early- and late-replicating chromosomal domains were pulse-labeled with halogenated nucleotides and prelabeled cells were synchronized at various times during the following G1-phase. The recruitment of Mcm2 and RPA to these domains was examined in relation to the formation of a nuclear envelope, specification of the dihydrofolate reductase (DHFR) replication origin and entry into S-phase. Mcm2 was loaded gradually and cumulatively onto both early- and late-replicating chromatin from late telophase throughout G1-phase. During S-phase, detectable Mcm2 was rapidly excluded from PCNA-containing active replication forks. By contrast, detergent-resistant RPA foci were undetectable until the onset of S-phase, when RPA joined only the earliest-firing replicons. During S-phase, RPA was present with PCNA specifically at active replication forks. Together, our data are consistent with a role for Mcm proteins, but not RPA, in the formation of mammalian pre-RCs during early G1-phase.

HsMCM2/BM28: a novel proliferation marker for human tumors and normal tissues.

HsMCM2/BM28 is a member of the family of minichromosome maintenance (MCM) proteins, which play a critical role in DNA replication by helping to ensure that DNA is replicated once and only once per cell cycle. The association of HsMCM2 with DNA replication suggested to us that it might prove useful as a new marker for cell proliferation. To test this possibility, we employed immunohistochemistry and immunoblotting to study HsMCM2 expression in both normal human tissues and primary human tumors. We found that HsMCM2 was detectable by immunoblotting in 97% of the studied tumors but in only 27% of the corresponding normal tissues. In normal tissues, the immunoblot signal was weaker than in tumors. Immunohistochemistry revealed that in normal tissues HsMCM2 is present only in proliferating cell nuclei. In most cases, tumor cell nuclei produced a stronger HsMCM2 signal than normal proliferating cell nuclei. Comparative studies revealed that antibodies against HsMCM2 stained fewer nuclei than antibodies against proliferating cell nuclear antigen but usually more than antibodies against Ki-67 (another proliferation-related antigen). Thus, the correlations between proliferation and antigenic signal are different for these three proteins. These results indicate that HsMCM2 is, indeed, a novel marker for proliferating cells. Further studies are required to determine whether the fact that HsMCM2 has a different correlation with proliferation and elevated staining intensity in tumor nuclei (compared to nuclei in normal proliferating cells) will permit it to be a more useful diagnostic and prognostic marker than proliferating cell nuclear antigen and Ki-67.

Experimental induction of prenucleolar bodies (PNBs) in interphase cells: interphase PNBs show similar characteristics as those typically observed at telophase of mitosis in untreated cells.

Recently, it was shown that a short exposure of living mammalian cells to low ionic strength buffers (hypotonic shock) caused partial or almost complete unraveling of interphase nucleoli. However, when the cells were released from the hypotonic shock and transferred to normal isotonic medium, functionally active and structurally integral nucleoli were reassembled at their initial positions within interphase nuclei. Here, we show further that this process is accompanied by the appearance of numerous discrete extranucleolar bodies, which have striking similarities to the prenucleolar bodies (PNBs) observed in untreated cells at telophase of mitosis. (1) Like PNBs at mitosis, hypotonically induced interphase PNBs are composed of RNA-positive granules and fibrils, contain the major nucleolar protein B23 and silver-binding proteins, but lack DNA and RNA polymerase I transcription factor UBF. (2) As for mitotic PNBs, disappearance of the interphase PNB counterparts coincides with the increase in size of reconstructed nucleoli. (3) Addition of actinomycin D does not prevent assembly of interphase PNBs, but does arrest their coalescence with the chromosomal nucleolus-organizing regions and blocks the complete reformation of nucleoli. It is concluded that the assembly of PNBs generally observed at telophase of mitosis can be induced experimentally in nuclei of interphase mammalian cells in vivo. At interphase, this process is probably initiated by changes in the intracellular ionic environment.

Cell cycle-dependent translocations of a major nucleolar phosphoprotein, B23, and some characteristics of its variants.

A major nucleolar phosphoprotein, B23, is thought to play several apparently unrelated roles and appears to be associated with other cell compartments besides the nucleolus. However, characteristic properties of B23 variants still remain to be established. Here, we raised a new monoclonal antibody against B23 (20B2) and used it to address the issue particularly focusing on the events during mitosis. Also, we made an attempt to generalize the data on the cell cycle-dependent translocations of B23 by the use of three mammalian cell lines (HeLa, PK, RAMT) which were found to be immunoreactive for 20B2. In all the cell strains studied, B23 was chiefly located within the nucleolus at interphase, and was associated with a few cellular domains during mitosis. They were: the nucleoplasm (at prophase before the nuclear envelope breakdown), the cytoplasm (from prometaphase until mid telophase), the perichromosomal layer (from prometaphase till early telophase), cytoplasmic B23-containing bodies (at anaphase and telophase) and prenucleolar bodies, PNBs (at telophase). On Western blots, electrophoretic mobility of B23 was found to be the same at G1, S and G2 periods of interphase, but became slower at mitosis. In situ and cell extraction experiments showed that like the nucleolar B23, B23 of the perichromosomal layer and that of PNBs was highly resistant to extraction with Triton X-100, but could be released with Triton X-100/RNase A. These findings indicated that these portions of B23 were most likely to be associated with RNA. The cytoplasmic B23 was the major intracellular variant of B23 during mitosis. It had a slightly lower electrophoretic mobility than the perichromosomal B23 and could readily be extracted with Triton X-100 without addition of RNase A, a fact indicating that the cytoplasmic B23 was mainly in an RNA-free state. Mitosis-like translocations of B23 from the nucleolus to the nucleoplasm induced by actinomycin D increased its extractability but did not affect the electrophoretic mobility. The phosphorylation status of different B23 variants at interphase and mitosis both in controls and following the drug, is discussed.

Large, complex modular structure of a fission yeast DNA replication origin.

BACKGROUND: In the budding yeast, Saccharomyces cerevisiae, each DNA replication origin is associated with an autonomously replicating sequence (ARS) element. Each element contains several modules, including an essential close match to the 11 base-pair (bp) ARS consensus sequence (ACS) and two or three short (< 20 bp) stimulatory motifs, within a stretch of approximately 150 bp or less. To determine whether a similar origin structure exists in the evolutionarily distant fission yeast, Schizosaccharomyces pombe, we used deletion and linker substitution scanning to identify the sequences important for the function of ars3002, a chromosomal replication origin. RESULTS: We detected two large (30-55 bp) essential regions and several additional stimulatory sequences within a 600 bp stretch of a restriction fragment containing ars3002. The two essential regions are similar to each other, and sequences similar to them are found in all known S. pombe ARS elements, suggesting that one or both of them may represent the S. pombe equivalent of the S. cerevisiae ACS. CONCLUSIONS: Like S. cerevisiae origins, the S. pombe origin, ars3002, possesses a modular structure, but the number and size of modules is greater for ars3002, and ars3002 is larger than S. cerevisiae origins. These observations suggest that origin function in S. pombe requires more protein-DNA interactions than in S. cerevisiae.