Invariant dynamics in a united-atom model of an ionic liquid.

We study a united-atom model of the ionic liquid 1-butyl-1-methylpyrrolidinium bis(trifluoromethyl)sulfonylamide to determine to what extent there exist curves in the phase diagram along which the microscopic dynamics are invariant when expressed in dimensionless, or reduced, form. The initial identification of these curves, termed isodynes, is made by noting that contours of reduced shear viscosity and reduced self-diffusion coefficient coincide to a good approximation. Choosing specifically the contours of reduced viscosity as nominal isodynes, further simulations were carried out for state points on these, and other aspects of dynamics were investigated to study their degree of invariance. These include the mean-squared displacement, shear-stress autocorrelation function, and various rotational correlation functions. These were invariant to a good approximation, with the main exception being rotations of the anion about its long axis. The dynamical features that are invariant have in common that they are aspects that would be relevant for a coarse-grained description of the system; specifically, removing the most microscopic degrees of freedom in principle leads to a simplification of the potential energy landscape, which allows for the existence of isodynes.

Revisiting fecal metatranscriptomics analyses of macaques with idiopathic chronic diarrhoea with a focus on trichomonad parasites.

Trichomonads, anaerobic microbial eukaryotes members of the phylum Parabasalia, are common obligate extracellular symbionts that can lead to pathological or asymptomatic colonization of various mucosal surfaces in a wide range of animal hosts. Results from previous in vitro studies have suggested a number of intriguing mucosal colonization strategies by Trichomonads, notably highlighting the importance of interactions with bacteria. However, in vivo validation is currently lacking. A previous metatranscriptomics study into the cause of idiopathic chronic diarrhoea in macaques reported the presence of an unidentified protozoan parasite related to Trichomonas vaginalis. In this work, we performed a reanalysis of the published data in order to identify the parasite species present in the macaque gut. We also leveraged the information-rich metatranscriptomics data to investigate the parasite behaviour in vivo. Our results indicated the presence of at least 3 genera of Trichomonad parasite; Tetratrichomonas, Pentatrichomonas and Trichomitus, 2 of which had not been previously reported in the macaque gut. In addition, we identified common in vivo expression profiles shared amongst the Trichomonads. In agreement with previous findings for other Trichomonads, our results highlighted a relationship between Trichomonads and mucosal bacterial diversity which could be influential in health and disease.

Sporadic isolation of Tetratrichomonas species from the cattle urogenital tract.

Tritrichomonas foetus is a venereal trichomonad parasite which causes reproductive issues in cattle. No other trichomonads are known to be urogenital pathogens in cattle, but there are several reports of Tetratrichomonas and Pentatrichomonas isolates of unclear origin from the cattle urogenital tract (UGT) in the Americas. This study reports the first case of a non-T. foetus cattle urogenital trichomonad isolate in Europe. Molecular analysis of the internal transcribed spacer (ITS) 1-5.8S ribosomal RNA-ITS 2 and 18S ribosomal RNA loci suggest that the isolate is a Tetratrichomonas species from a lineage containing other previously described bull preputial isolates. We identified close sequence similarity between published urogenital and gastrointestinal Tetratrichomonas spp., and this is reviewed alongside further evidence regarding the gastrointestinal origin of non-T. foetus isolates. Routine screening for T. foetus is based on culture and identification by microscopy, and so considering other trichomonad parasites of the bovine UGT is important to avoid misdiagnosis.

Quantifying dynamical and structural invariance in a simple molten salt model.

Recent experimental results for the structure in the ionic liquid PYR14 +TFSI- have shown invariance in the main structure factor peak along curves of equal electrical conductivity [Hansen et al., Phys. Chem. Chem. Phys. 22, 14169 (2020)]. The charge peak decreases slightly with increasing temperature at fixed conductivity, however. For simple liquids, curves with invariant dynamics and structure, known as isomorphs, can be identified as configurational adiabats. While liquids with strong-Coulomb interactions do not have good isomorphs, ionic liquids could be an intermediate case with approximate isomorphs along which some aspects of structure and dynamics are invariant. We study a simple molten salt model using molecular dynamics simulations to test this hypothesis. Simple measures of structure and dynamics are investigated along with one transport property, the shear viscosity. We find that there is a substantial degree of invariance of the self-intermediate scattering function, the mean square displacement, and the viscosity along configurational adiabats over a wide range of densities for the three adiabats simulated. The density range studied is more than a factor of two and extends from the strong-Coulomb regime at low densities to the weak-Coulomb regime at high densities. The structure is not invariant over the full range of density, but in the weak-Coulomb regime, we see behavior similar to that seen experimentally over density changes of order 15%. In view of the limited structural invariance but substantial dynamical invariance, we designate the configurational adiabats as isodynes.

Non-Newtonian behavior and molecular structure of Cooee bitumen under shear flow: A non-equilibrium molecular dynamics study.

The rheology and molecular structure of a model bitumen (Cooee bitumen) under shear are investigated in the non-Newtonian regime using non-equilibrium molecular dynamics simulations. The shear viscosity, normal stress differences, and pressure of the bitumen mixture are computed at different shear rates and different temperatures. The model bitumen is shown to be a shear-thinning fluid at all temperatures. In addition, the Cooee model is able to reproduce experimental results showing the formation of nanoaggregates composed of stacks of flat aromatic molecules in bitumen. These nanoaggregates are immersed in a solvent of saturated hydrocarbon molecules. At a fixed temperature, the shear-shinning behavior is related not only to the inter- and intramolecular alignments of the solvent molecules but also to the decrease of the average size of the nanoaggregates at high shear rates. The variation of the viscosity with temperature at different shear rates is also related to the size and relative composition of the nanoaggregates. The slight anisotropy of the whole sample due to the nanoaggregates is considered and quantified. Finally, the position of bitumen mixtures in the broad literature of complex systems such as colloidal suspensions, polymer solutions, and associating polymer networks is discussed.

Estimating the density-scaling exponent of a monatomic liquid from its pair potential.

This paper investigates two conjectures for calculating the density dependence of the density-scaling exponent γ of a single-component, pair-potential liquid with strong virial potential-energy correlations. The first conjecture gives an analytical expression for γ directly in terms of the pair potential. The second conjecture is a refined version of this involving the most likely nearest-neighbor distance determined from the pair-correlation function. The conjectures are tested by simulations of three systems, one of which is the standard Lennard-Jones liquid. While both expressions give qualitatively correct results, the second is more accurate.

Comparative genomics between Trichomonas tenax and Trichomonas vaginalis: CAZymes and candidate virulence factors.

Introduction: The oral trichomonad Trichomonas tenax is increasingly appreciated as a likely contributor to periodontitis, a chronic inflammatory disease induced by dysbiotic microbiota, in humans and domestic animals and is strongly associated with its worst prognosis. Our current understanding of the molecular basis of T. tenax interactions with host cells and the microbiota of the oral cavity are still rather limited. One laboratory strain of T. tenax (Hs-4:NIH/ATCC 30207) can be grown axenically and two draft genome assemblies have been published for that strain, although the structural and functional annotation of these genomes is not available. Methods: GenSAS and Galaxy were used to annotate two publicly available draft genomes for T. tenax, with a focus on protein-coding genes. A custom pipeline was used to annotate the CAZymes for T. tenax and the human sexually transmitted parasite Trichomonas vaginalis, the most well-characterized trichomonad. A combination of bioinformatics analyses was used to screen for homologs of T. vaginalis virulence and colonization factors within the T. tenax annotated proteins. Results: Our annotation of the two T. tenax draft genome sequences and their comparison with T. vaginalis proteins provide evidence for several candidate virulence factors. These include candidate surface proteins, secreted proteins and enzymes mediating potential interactions with host cells and/or members of the oral microbiota. The CAZymes annotation identified a broad range of glycoside hydrolase (GH) families, with the majority of these being shared between the two Trichomonas species. Discussion: The presence of candidate T. tenax virulence genes supports the hypothesis that this species is associated with periodontitis through direct and indirect mechanisms. Notably, several GH proteins could represent potential new virulence factors for both Trichomonas species. These data support a model where T. tenax interactions with host cells and members of the oral microbiota could synergistically contribute to the damaging inflammation characteristic of periodontitis, supporting a causal link between T. tenax and periodontitis.

Statistical mechanics of Roskilde liquids: configurational adiabats, specific heat contours, and density dependence of the scaling exponent.

We derive exact results for the rate of change of thermodynamic quantities, in particular, the configurational specific heat at constant volume, CV, along configurational adiabats (curves of constant excess entropy Sex). Such curves are designated isomorphs for so-called Roskilde liquids, in view of the invariance of various structural and dynamical quantities along them. The slope of the isomorphs in a double logarithmic representation of the density-temperature phase diagram, γ, can be interpreted as one third of an effective inverse power-law potential exponent. We show that in liquids where γ increases (decreases) with density, the contours of CV have smaller (larger) slope than configurational adiabats. We clarify also the connection between γ and the pair potential. A fluctuation formula for the slope of the CV-contours is derived. The theoretical results are supported with data from computer simulations of two systems, the Lennard-Jones fluid, and the Girifalco fluid. The sign of dγ∕dρ is thus a third key parameter in characterizing Roskilde liquids, after γ and the virial-potential energy correlation coefficient R. To go beyond isomorph theory we compare invariance of a dynamical quantity, the self-diffusion coefficient, along adiabats and CV-contours, finding it more invariant along adiabats.

Isomorph invariance of Couette shear flows simulated by the SLLOD equations of motion.

Non-equilibrium molecular dynamics simulations were performed to study the thermodynamic, structural, and dynamical properties of the single-component Lennard-Jones and the Kob-Andersen binary Lennard-Jones liquids. Both systems are known to have strong correlations between equilibrium thermal fluctuations of virial and potential energy. Such systems have good isomorphs (curves in the thermodynamic phase diagram along which structural, dynamical, and some thermodynamic quantities are invariant when expressed in reduced units). The SLLOD equations of motion were used to simulate Couette shear flows of the two systems. We show analytically that these equations are isomorph invariant provided the reduced strain rate is fixed along the isomorph. Since isomorph invariance is generally only approximate, a range of strain rates were simulated to test for the predicted invariance, covering both the linear and nonlinear regimes. For both systems, when represented in reduced units the radial distribution function and the intermediate scattering function are identical for state points that are isomorphic. The strain-rate dependent viscosity, which exhibits shear thinning, is also invariant along an isomorph. Our results extend the isomorph concept to the non-equilibrium situation of a shear flow, for which the phase diagram is three dimensional because the strain rate defines a third dimension.

Isomorphs in sheared binary Lennard-Jones glass: Transient response.

We have studied shear deformation of binary Lennard-Jones glasses to investigate the extent to which the transient part of the stress strain curves is invariant when the thermodynamic state point is varied along an isomorph. Shear deformations were carried out on glass samples of varying stability, determined by cooling rate, and at varying strain rates, at state points deep in the glass. Density changes up to and exceeding a factor of two were made. We investigated several different methods for generating isomorphs but none of the previously developed methods could generate sufficiently precise isomorphs given the large density changes and nonequilibrium situation. Instead, the temperatures for these higher densities were chosen to give state points isomorphic to the starting state point by requiring the steady-state flow stress for isomorphic state points to be invariant in reduced units. In contrast to the steady-state flow stress, we find that the peak stress on the stress strain curve is not invariant. The peak stress decreases by a few percent for each ten percent increase in density, although the differences decrease with increasing density. Analysis of strain profiles and nonaffine motion during the transient phase suggests that the root of the changes in peak stress is a varying tendency to form shear bands, with the largest tendency occurring at the lowest densities. We suggest that this reflects the effective steepness of the potential; a higher effective steepness gives a greater tendency to form shear bands.

Evolutionary conservation of Trichomonas-mycoplasma symbiosis across the host species barrier.

Introduction: The protozoan parasite Trichomonas vaginalis is the most common cellular sexually transmitted disease in humans, and the closely related species Trichomonas gallinae is an avian parasite of ecological and economic importance. Phylogenetic evidence suggests T. vaginalis arose during bird to human transmission of a T. gallinae-like ancestor. Trichomonas vaginalis shares a strong clinical association with the independent sexually transmitted pathogen Metamycoplasma (formerly Mycoplasma) hominis, and the uncultured bacterium "Candidatus Malacoplasma (formerly Mycoplasma) girerdii," with the latter association being an order of magnitude stronger. Both bacterial species have been shown to profoundly influence T. vaginalis growth, energy production and virulence-associated mechanisms. Methods: Evidence for a novel Malacoplasma sp. was discovered by in vivo Illumina metatranscriptomics sequencing of the T. gallinae-infected pigeon mouth. We leveraged published 16S rDNA profiling data from digestive tract of 12 healthy and 24 T. gallinae-infected pigeons to investigate association between the novel Malacoplasma sp. and T. gallinae. We utilised Illumina metagenomics sequencing targeted to pigeon oral and crop samples infected with the novel Malacoplasma sp. to generate its full-length genome sequence. Sequence similarity network analysis was used to compare annotated proteins from the novel Malacoplasma sp. with a range of other related species. Results: Here we present evidence for a novel Malacoplasma species, related to "Ca. M. girerdii," that is strongly associated with T. gallinae in the upper digestive tract of domestic pigeons. Analysis of the genome sequence revealed gene features apparently specific to a Trichomonas-symbiotic Malacoplasma lineage. Discussion: These data support a model of long-term association between Trichomonas and Malacoplasma spp. that has been conserved across diversification of the Trichomonas lineage and the host species barrier from birds to human.

Identification of D-arabinan-degrading enzymes in mycobacteria.

Bacterial cell growth and division require the coordinated action of enzymes that synthesize and degrade cell wall polymers. Here, we identify enzymes that cleave the D-arabinan core of arabinogalactan, an unusual component of the cell wall of Mycobacterium tuberculosis and other mycobacteria. We screened 14 human gut-derived Bacteroidetes for arabinogalactan-degrading activities and identified four families of glycoside hydrolases with activity against the D-arabinan or D-galactan components of arabinogalactan. Using one of these isolates with exo-D-galactofuranosidase activity, we generated enriched D-arabinan and used it to identify a strain of Dysgonomonas gadei as a D-arabinan degrader. This enabled the discovery of endo- and exo-acting enzymes that cleave D-arabinan, including members of the DUF2961 family (GH172) and a family of glycoside hydrolases (DUF4185/GH183) that display endo-D-arabinofuranase activity and are conserved in mycobacteria and other microbes. Mycobacterial genomes encode two conserved endo-D-arabinanases with different preferences for the D-arabinan-containing cell wall components arabinogalactan and lipoarabinomannan, suggesting they are important for cell wall modification and/or degradation. The discovery of these enzymes will support future studies into the structure and function of the mycobacterial cell wall.

Two Different Species of Mycoplasma Endosymbionts Can Influence Trichomonas vaginalis Pathophysiology.

Trichomonas vaginalis can host the endosymbiont Mycoplasma hominis, an opportunistic pathogenic bacterium capable of modulating T. vaginalis pathobiology. Recently, a new noncultivable mycoplasma, "Candidatus Mycoplasma girerdii," has been shown to be closely associated with women affected by trichomoniasis, suggesting a biological association. Although several features of "Ca. M. girerdii" have been investigated through genomic analysis, the nature of the potential T. vaginalis-"Ca. M. girerdii" consortium and its impact on the biology and pathogenesis of both microorganisms have not yet been explored. Here, we investigate the association between "Ca. M. girerdii" and T. vaginalis isolated from patients affected by trichomoniasis, demonstrating their intracellular localization. By using an in vitro model system based on single- and double-Mycoplasma infection of Mycoplasma-free isogenic T. vaginalis, we investigated the ability of the protist to establish a relationship with the bacteria and impact T. vaginalis growth. Our data indicate likely competition between M. hominis and "Ca. M. girerdii" while infecting trichomonad cells. Comparative dual-transcriptomics data showed major shifts in parasite gene expression in response to the presence of Mycoplasma, including genes associated with energy metabolism and pathogenesis. Consistent with the transcriptomics data, both parasite-mediated hemolysis and binding to host epithelial cells were significantly upregulated in the presence of either Mycoplasma species. Taken together, these results support a model in which this microbial association could modulate the virulence of T. vaginalis. IMPORTANCE T. vaginalis and M. hominis form a unique case of endosymbiosis that modulates the parasite's pathobiology. Recently, a new nonculturable mycoplasma species ("Candidatus Mycoplasma girerdii") has been described as closely associated with the protozoon. Here, we report the characterization of this endosymbiotic relationship. Clinical isolates of the parasite demonstrate that mycoplasmas are common among trichomoniasis patients. The relationships are studied by devising an in vitro system of single and/or double infections in isogenic protozoan recipients. Comparative growth experiments and transcriptomics data demonstrate that the composition of different microbial consortia influences the growth of the parasite and significantly modulates its transcriptomic profile, including metabolic enzymes and virulence genes such as adhesins and pore-forming proteins. The data on modulation from RNA sequencing (RNA-Seq) correlated closely with those of the cytopathic effect and adhesion to human target cells. We propose the hypothesis that the presence and the quantitative ratios of endosymbionts may contribute to modulating protozoan virulence. Our data highlight the importance of considering pathogenic entities as microbial ecosystems, reinforcing the importance of the development of integrated diagnostic and therapeutic strategies.

Effect of the Symbiosis with Mycoplasma hominis and Candidatus Mycoplasma Girerdii on Trichomonas vaginalis Metronidazole Susceptibility.

Trichomoniasis, the most common non-viral sexually transmitted infection worldwide, is caused by the protozoon Trichomonas vaginalis. The 5- nitroimidazole drugs, of which metronidazole is the most prescribed, are the only effective drugs to treat trichomoniasis. Resistance against metronidazole is increasingly reported among T. vaginalis isolates. T. vaginalis can establish an endosymbiosis with two Mycoplasma species, Mycoplasma hominis and Candidatus Mycoplasma girerdii, whose presence has been demonstrated to influence several aspects of the protozoan pathobiology. The role of M. hominis in T. vaginalis resistance to metronidazole is controversial, while the influence of Ca. M. girerdii has never been investigated. In this work, we investigate the possible correlation between the presence of Ca. M. girerdii and/or M. hominis and the in vitro drug susceptibility in a large group of T. vaginalis isolated in Italy and in Vietnam. We also evaluated, via RNA-seq analysis, the expression of protozoan genes involved in metronidazole resistance in a set of syngenic T. vaginalis strains, differing only for the presence/absence of the two Mycoplasmas. Our results show that the presence of M. hominis significantly increases the sensitivity to metronidazole in T. vaginalis and affects gene expression. On the contrary, the symbiosis with Candidatus Mycoplasma girerdii seems to have no effect on metronidazole resistance in T. vaginalis.

Pressure-energy correlations in liquids. V. Isomorphs in generalized Lennard-Jones systems.

This series of papers is devoted to identifying and explaining the properties of strongly correlating liquids, i.e., liquids with more than 90% correlation between their virial W and potential energy U fluctuations in the NVT ensemble. Paper IV [N. Gnan et al., J. Chem. Phys. 131, 234504 (2009)] showed that strongly correlating liquids have "isomorphs," which are curves in the phase diagram along which structure, dynamics, and some thermodynamic properties are invariant in reduced units. In the present paper, using the fact that reduced-unit radial distribution functions are isomorph invariant, we derive an expression for the shapes of isomorphs in the WU phase diagram of generalized Lennard-Jones systems of one or more types of particles. The isomorph shape depends only on the Lennard-Jones exponents; thus all isomorphs of standard Lennard-Jones systems (with exponents 12 and 6) can be scaled onto a single curve. Two applications are given. One tests the prediction that the solid-liquid coexistence curve follows an isomorph by comparing to recent simulations by Ahmed and Sadus [J. Chem. Phys. 131, 174504 (2009)]. Excellent agreement is found on the liquid side of the coexistence curve, whereas the agreement is less convincing on the solid side. A second application is the derivation of an approximate equation of state for generalized Lennard-Jones systems by combining the isomorph theory with the Rosenfeld-Tarazona expression for the temperature dependence of the potential energy on isochores. It is shown that the new equation of state agrees well with simulations.

Pressure-energy correlations in liquids. III. Statistical mechanics and thermodynamics of liquids with hidden scale invariance.

In this third paper of the series, which started with Bailey et al. [J. Chem. Phys. 129, 184507 (2008); ibid. 129, 184508 (2008)], we continue the development of the theoretical understanding of strongly correlating liquids--those whose instantaneous potential energy and virial are more than 90% correlated in their thermal equilibrium fluctuations at constant volume. The existence of such liquids was detailed in previous work, which identified them, based on computer simulations, as a large class of liquids, including van der Waals liquids but not, e.g., hydrogen-bonded liquids. We here discuss the following: (1) the scaling properties of inverse power-law and extended inverse power-law potentials (the latter includes a linear term that "hides" the approximate scale invariance); (2) results from computer simulations of molecular models concerning out-of-equilibrium conditions; (3) ensemble dependence of the virial/potential-energy correlation coefficient; (4) connection to the Grüneisen parameter; and (5) interpretation of strong correlations in terms of the energy-bond formalism.

Pressure-energy correlations in liquids. IV. "Isomorphs" in liquid phase diagrams.

This paper is the fourth in a series devoted to identifying and explaining the properties of strongly correlating liquids, i.e., liquids where virial and potential energy correlate better than 90% in their thermal equilibrium fluctuations in the NVT ensemble. For such liquids we here introduce the concept of "isomorphic" curves in the phase diagram. A number of thermodynamic, static, and dynamic isomorph invariants are identified. These include the excess entropy, the isochoric specific heat, reduced-unit static and dynamic correlation functions, as well as reduced-unit transport coefficients. The dynamic invariants apply for both Newtonian and Brownian dynamics. It is shown that after a jump between isomorphic state points the system is instantaneously in thermal equilibrium; consequences of this for generic aging experiments are discussed. Selected isomorph predictions are validated by computer simulations of the Kob-Andersen binary Lennard-Jones mixture, which is a strongly correlating liquid. The final section of the paper relates the isomorph concept to phenomenological melting rules, Rosenfeld's excess entropy scaling, Young and Andersen's approximate scaling principle, and the two-order parameter maps of Debenedetti and co-workers. This section also shows how the existence of isomorphs implies an "isomorph filter" for theories for the non-Arrhenius temperature dependence of viscous liquids' relaxation time, and it explains isochronal superposition for strongly correlating viscous liquids.

Hidden scale invariance at high pressures in gold and five other face-centered-cubic metal crystals.

Recent density functional theory simulations showed that metals have a hitherto overlooked symmetry termed "hidden scale invariance" [Hummel et al., Phys. Rev. B 92, 174116 (2015)PRBMDO1098-012110.1103/PhysRevB.92.174116]. This scaling property implies the existence of lines in the thermodynamic phase diagram, so-called isomorphs, along which structure and dynamics are invariant to a good approximation when given in properly reduced units. This means that the phase diagram becomes effectively one-dimensional with regard to several physical properties. This paper investigates consequences and implications of the isomorph theory in six metallic crystals: Au, Ni, Cu, Pd, Ag, and Pt. The data are obtained from molecular dynamics simulations employing many-body effective medium theory (EMT) to model the atomic interactions realistically. We test the predictions from isomorph theory for structure and dynamics by means of the radial distribution and the velocity autocorrelation functions, as well as the prediction of instantaneous equilibration after a jump between two isomorphic state points. Many properties of crystals tend to be dominated by defects, and many of the properties associated with these defects are expected to be isomorph invariant as well. This is investigated in this paper for the case of vacancy diffusion. In regard to the perfect crystal properties, we find the predicted invariance of structure and also, though less perfectly, of dynamics. We show results on the variation of the density-scaling exponent γ, which can be related to the Grüneisen parameter, for all six metals. We consider large density changes up to a factor of two, corresponding to very high pressures. Unlike systems modeled using the Lennard-Jones potential where the density-scaling exponent γ is almost constant, this quantity varies substantially when using the EMT potential and is also strongly material dependent.

Isomorph invariance of dynamics of sheared glassy systems.

We study hidden scale invariance in the glassy phase of the Kob-Andersen binary Lennard-Jones system. After cooling below the glass transition, we generate a so-called isomorph from the fluctuations of potential energy and virial in the NVT ensemble: a set of density, temperature pairs for which structure and dynamics are identical when expressed in appropriate reduced units. To access dynamical features, we shear the system using the SLLOD algorithm coupled with Lees-Edwards boundary conditions and study the statistics of stress fluctuations and the particle displacements transverse to the shearing direction. We find good collapse of the statistical data, showing that isomorph theory works well in this regime. The analysis of stress fluctuations, in particular the distribution of stress changes over a given strain interval, allows us to identify a clear signature of avalanche behavior in the form of an exponential tail on the negative side. This feature is also isomorph invariant. The implications of isomorphs for theories of plasticity are discussed briefly.

Pressure-energy correlations in liquids. I. Results from computer simulations.

We show that a number of model liquids at fixed volume exhibit strong correlations between equilibrium fluctuations of the configurational parts of (instantaneous) pressure and energy. We present detailed results for 13 systems, showing in which systems these correlations are significant. These include Lennard-Jones liquids (both single- and two-component) and several other simple liquids, neither hydrogen-bonding liquids such as methanol and water, nor the Dzugutov liquid, which has significant contributions to pressure at the second nearest neighbor distance. The pressure-energy correlations, which for the Lennard-Jones case are shown to also be present in the crystal and glass phases, reflect an effective inverse power-law potential dominating fluctuations, even at zero and slightly negative pressure. An exception to the inverse power-law explanation is a liquid with hard-sphere repulsion and a square-well attractive part, where a strong correlation is observed, but only after time averaging. The companion paper [N. P. Bailey et al., J. Chem. Phys. 129, 184508 (2008)] gives a thorough analysis of the correlations, with a focus on the Lennard-Jones liquid, and a discussion of some experimental and theoretical consequences.