Simulations in the era of exascale computing.

Exascale computers - supercomputers that can perform 1018 floating point operations per second - started coming online in 2022: in the United States, Frontier launched as the first public exascale supercomputer and Aurora is due to open soon; OceanLight and Tianhe-3 are operational in China; and JUPITER is due to launch in 2023 in Europe. Supercomputers offer unprecedented opportunities for modelling complex materials. In this Viewpoint, five researchers working on different types of materials discuss the most promising directions in computational materials science.

Molecular basis of conformational changes and mechanics of integrins.

Integrin, as a mechanotransducer, establishes the mechanical reciprocity between the extracellular matrix (ECM) and cells at integrin-mediated adhesion sites. This study used steered molecular dynamics (SMD) simulations to investigate the mechanical responses of integrin αvß3 with and without 10th type III fibronectin (FnIII10) binding for tensile, bending and torsional loading conditions. The ligand-binding integrin confirmed the integrin activation during equilibration and altered the integrin dynamics by changing the interface interaction between ß-tail, hybrid and epidermal growth factor domains during initial tensile loading. The tensile deformation in integrin molecules indicated that fibronectin ligand binding modulates its mechanical responses in the folded and unfolded conformation states. The bending deformation responses of extended integrin models reveal the change in behaviour of integrin molecules in the presence of Mn2+ ion and ligand based on the application of force in the folding and unfolding directions of integrin. Furthermore, these SMD simulation results were used to predict the mechanical properties of integrin underlying the mechanism of integrin-based adhesion. The evaluation of integrin mechanics provides new insights into understanding the mechanotransmission (force transmission) between cells and ECM and contributes to developing an accurate model for integrin-mediated adhesion. This article is part of a discussion meeting issue 'Supercomputing simulations of advanced materials'.

Interstitial fluid flow contributes to prostate cancer invasion and migration to bone; study conducted using a novel horizontal flow bioreactor.

Prostate cancer bone metastasis is the leading cause of cancer-related mortality in men in the United States, causing severe damage to skeletal tissue. The treatment of advanced-stage prostate cancer is always challenging due to limited drug treatment options, resulting in low survival rates. There is a scarcity of knowledge regarding the mechanisms associated with the effects of biomechanical cues by the interstitial fluid flow on prostate cancer cell growth and migration. We have designed a novel bioreactor system to demonstrate the impact of interstitial fluid flow on the migration of prostate cancer cells to the bone during extravasation. First, we demonstrated that a high flow rate induces apoptosis in PC3 cells via TGF-ß1 mediated signaling; thus, physiological flow rate conditions are optimum for cell growth. Next, to understand the role of interstitial fluid flow in prostate cancer migration, we evaluated the migration rate of cells under static and dynamic conditions in the presence or absence of bone. We report that CXCR4 levels were not significantly changed under static and dynamic conditions, indicating that CXCR4 activation in PC3 cells is not influenced by flow conditions but by the bone, where CXCR4 levels were upregulated. The bone-upregulated CXCR4 levels led to increased MMP-9 levels resulting in a high migration rate in the presence of bone. In addition, upregulated levels ofαvß3integrins under fluid flow conditions contributed to an overall increase in the migration rate of PC3 cells. Overall, this study demonstrates the potential role of interstitial fluid flow in prostate cancer invasion. Understanding the critical role of interstitial fluid flow in promoting prostate cancer cell progression will enhance current therapies for advanced-stage prostate cancer and provide improved treatment options for patients.

Nanoclays in medicine: a new frontier of an ancient medical practice.

Clays have been used as early as 2500 BC in human civilization for medicinal purposes. The ease of availability, biocompatibility, and versatility of these unique charged 2D structures abundantly available in nature have enabled the extensive applications of clays in human history. Recent advances in the use of clays in nanostructures and as components of polymer clay nanocomposites have exponentially expanded the use of clays in medicine. This review covers the details of structures and biomedical applications of several common clays, including montmorillonite, LAPONITE®, kaolinite, and halloysite. Here we describe the applications of these clays in wound dressings as hemostatic agents in drug delivery of drugs for cancer and other diseases and tissue engineering. Also reviewed are recent experimental and modeling studies that elucidate the impact of clay structures on cellular processes and cell adhesion processes. Various mechanisms of clay-mediated bioactivity, including protein localization, modulation of cell adhesion, biomineralization, and the potential of clay nanoparticles to impact cell differentiation, are presented. We also review the current developments in understanding the impact of clays on cellular responses. This review also elucidates new emerging areas of use of nanoclays in osteogenesis and the development of in vitro models of bone metastasis of cancer.

Molecular and structural basis of actin filament severing by ADF/cofilin.

ADF/cofilin's cooperative binding to actin filament modifies the conformation and alignment of G-actin subunits locally, causing the filament to sever at "boundaries" formed among bare and ADF/cofilin-occupied regions. Analysis of the impact of the ADF/cofilin cluster boundary on the deformation behavior of actin filaments in a mechanically strained environment is critical for understanding the biophysics of their severing. The present investigation uses molecular dynamics simulations to generate atomic resolution models of bare, partially, and fully cofilin decorated actin filaments. Steered molecular dynamics simulations are utilized to determine the mechanical properties of three filament models when subjected to axial stretching, axial compression, and bending forces. We highlight differences in strain distribution, failure mechanisms in the three filament models, and biomechanical effects of cofilin cluster boundaries in overall filament rupture. Based on the influence of ADF/cofilin binding on intrastrand and interstrand G-actin interfaces, the cofilin-mediated actin filament severing model proposed here can help understand cofilin mediated actin dynamics.

Label-free discrimination of tumorigenesis stages using in vitro prostate cancer bone metastasis model by Raman imaging.

Metastatic prostate cancer colonizes the bone to pave the way for bone metastasis, leading to skeletal complications associated with poor prognosis and morbidity. This study demonstrates the feasibility of Raman imaging to differentiate between cancer cells at different stages of tumorigenesis using a nanoclay-based three-dimensional (3D) bone mimetic in vitro model that mimics prostate cancer bone metastasis. A comprehensive study comparing the classification of as received prostate cancer cells in a two-dimensional (2D) model and cancer cells in a 3D bone mimetic environment was performed over various time intervals using principal component analysis (PCA). Our results showed distinctive spectral differences in Raman imaging between prostate cancer cells and the cells cultured in 3D bone mimetic scaffolds, particularly at 1002, 1261, 1444, and 1654 cm-1, which primarily contain proteins and lipids signals. Raman maps capture sub-cellular responses with the progression of tumor cells into metastasis. Raman feature extraction via cluster analysis allows for the identification of specific cellular constituents in the images. For the first time, this work demonstrates a promising potential of Raman imaging, PCA, and cluster analysis to discriminate between cancer cells at different stages of metastatic tumorigenesis.

A Coarse-Grained Model for the Mechanical Behavior of Na-Montmorillonite Clay.

Sodium montmorillonite (Na-MMT) is one of the most commonly found swelling clay minerals with diverse engineering and technological applications. The nanomechanical properties of this mineral have been extensively investigated computationally utilizing molecular dynamics (MD) simulations to portray the molecular-level changes at different environmental conditions. As the environmentally found Na-MMT clays are generally sized within hundreds of nanometers, all-atomistic (AA) MD simulations of clays within such size range are particularly challenging due to computational inefficiency. Informed from atomistic modeling, a coarse-grained (CG) modeling technique can be employed to overcome the spatiotemporal limitation. The current study presents a modeling strategy to develop a computationally efficient model of Na-MMT clay with a typical size over ≃100 nm by shrinking the atomistic platelet thickness and reducing the number of center-layer atoms. Using the "strain-energy conservation" approach, the force field parameters for the CG model are obtained and the developed CG model can well preserve in-plane tension, shear, and bending behaviors of atomistic counterparts. Remarkably, the CG tactoid model of Na-MMT, a hierarchical multilayer structure, can reproduce the interlayer shear and adhesion as well as d-spacing among the clay sheets as of atomistic one to a good approximation while gaining significantly improved computational speed. Our study demonstrates the efficacy of the CG modeling framework, paving the way for the bottom-up multiscale prediction of mechanical behaviors of clay and related minerals.

Nanoarchitectonics of a Microsphere-Based Scaffold for Modeling Neurodevelopment and Neurological Disease.

Three-dimensional cellular constructs derived from pluripotent stem cells allow the ex vivo study of neurodevelopment and neurological disease within a spatially organized model. However, the robustness and utility of three-dimensional models is impacted by tissue self-organization, size limitations, nutrient supply, and heterogeneity. In this work, we have utilized the principles of nanoarchitectonics to create a multifunctional polymer/bioceramic composite microsphere system for stem cell culture and differentiation in a chemically defined microenvironment. Microspheres could be customized to produce three-dimensional structures of defined size (ranging from >100 to <350 µm) with lower mechanical properties compared with a thin film. Furthermore, the microspheres softened in solution, approaching more tissue-like mechanical properties over time. With neural stem cells (NSCs) derived from human induced pluripotent stem cells, microsphere-cultured NSCs were able to utilize multiple substrates to promote cell adhesion and proliferation. Prolonged culture of NSC-bound microspheres under differentiating conditions allowed the formation of both neural and glial cell types from control and patient-derived stem cell models. Human NSCs and differentiated neurons could also be cocultured with astrocytes and human umbilical vein endothelial cells, demonstrating application for tissue-engineered modeling of development and human disease. We further demonstrated that microspheres allow the loading and sustained release of multiple recombinant proteins to support cellular maintenance and differentiation. While previous work has principally utilized self-organizing models or protein-rich hydrogels for neural culture, the three-dimensional matrix developed here through nanoarchitectonics represents a chemically defined and robust alternative for the in vitro study of neurodevelopment and nervous system disorders.

Binding of SARS-COV-2 (COVID-19) and SARS-COV to human ACE2: Identifying binding sites and consequences on ACE2 stiffness.

The SARS-CoV-2 coronavirus (COVID-19) that is causing the massive global pandemic exhibits similar human cell invasion mechanism as the coronavirus SARS-CoV, which had significantly lower fatalities. The cell membrane protein Angiotensin-converting enzyme 2 (ACE2) is the initiation point for both the coronavirus infections in humans. Here, we model the molecular interactions and mechanical properties of ACE2 with both SARS-CoV and COVID-19 spike protein receptor-binding domains (RBD). We report that the COVID-19 spike RBD interacts with ACE2 more strongly and at only two protein residues, as compared to multi-residue interaction of the SARS-CoV. Although both coronaviruses stiffen the ACE2, the impact of COVID-19 is six times larger, which points towards differences in the severity of the reported respiratory distress. The recognition of specific residues of ACE2 attachments to coronaviruses is important as the residues suggest potential sites of intervention to inhibit attachment and subsequent entry of the COVID-19 into human host cells.

Differences in Interactions Within Viral Replication Complexes of SARS-CoV-2 (COVID-19) and SARS-CoV Coronaviruses Control RNA Replication Ability.

COVID-19 has become a global pandemic caused by the SARS-CoV-2 coronavirus. SARS-CoV-2 shares many similarities with SARS coronavirus (SARS-CoV). A viral replication complex containing non-structural proteins (nsps) is the toolbox for RNA replication and transcription of both coronaviruses. In both cases, the RNA-dependent RNA polymerase (RdRp) domain of the coronaviral replication complex dictates the primary polymerase activity by cooperating with cofactors. The higher transmissibility and mortality due to SARS-CoV-2 are related to its higher RNA replication activity compared to SARS-CoV. The discrepancy between the RNA replication efficiency of SARS-CoV and SARS-CoV-2 can be understood by exploring interactions within their viral replication complexes. Our modeling of molecular interactions within the viral replication complexes of SARS-CoV and SARS-CoV-2 using molecular dynamics simulations suggests that in contrast to SARS-CoVnsp12, SARS-CoV2nsp12 prefers helices as the dominant interacting secondary motifs. The relative differences in nonbonded interactions between nsps could suggest viral RNA replication ability in coronaviruses. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11837-021-04662-6.

Nanostructured Biomaterials for In Vitro Models of Bone Metastasis Cancer.

In recent years, tissue engineering approaches have attracted substantial attention owing to their ability to create physiologically relevant in vitro disease models that closely mimic in vivo conditions. Here, we review nanocomposite materials and scaffolds used for the design of in vitro models of cancer, including metastatic sites. We discuss the role of material properties in modulating cellular phenotype in 3D disease models. Also, we highlight the application of tissue-engineered bone as a tool for faithful recapitulation of the microenvironment of metastatic prostate and breast cancer, since these two types of cancer have the propensity to metastasize to bone. Overall, we summarize recent efforts on developing 3D in vitro models of bone metastatic cancers that provide a platform to study tumor progression and facilitate high-throughput drug screening.

Evaluation of quasi-static and dynamic nanomechanical properties of bone-metastatic breast cancer cells using a nanoclay cancer testbed.

In recent years, there has been increasing interest in investigating the mechanical properties of individual cells to delineate disease mechanisms. Reorganization of cytoskeleton facilitates the colonization of metastatic breast cancer at bone marrow space, leading to bone metastasis. Here, we report evaluation of mechanical properties of two breast cancer cells with different metastatic ability at the site of bone metastases, using quasi-static and dynamic nanoindentation methods. Our results showed that the significant reduction in elastic modulus along with increased liquid-like behavior of bone metastasized MCF-7 cells was induced by depolymerization and reorganization of F-actin to the adherens junctions, whereas bone metastasized MDA-MB-231 cells showed insignificant changes in elastic modulus and F-actin reorganization over time, compared to their respective as-received counterparts. Taken together, our data demonstrate evolution of breast cancer cell mechanics at bone metastases.

Dissociation Mechanisms of G-actin Subunits Govern Deformation Response of Actin Filament.

Actin molecules are essential structural components of the cellular cytoskeleton. Here, we report a comprehensive analysis of F-actin's deformation behavior and highlight underlying mechanisms using steered molecular dynamics simulations (SMD). The investigation of F-actin was done under tension, compression, bending, and torsion. We report that the dissociation pattern of conformational locks at intrastrand and interstrand G-actin interfaces regulates the deformation response of F-actin. The conformational locks at the G-actin interfaces are portrayed by a spheroidal joint, interlocking serrated plates' analogy. Further, the SMD simulation approach was utilized to evaluate Young's modulus, flexural rigidity, persistent length, and torsional rigidity of F-actin, and the values obtained were found to be consistent with available experimental data. The evaluation of the mechanical properties of actin and the insight into the fundamental mechanisms contributing to its resilience described here are necessary for developing accurate models of eukaryotic cells and for assessing cellular viability and mobility.

Perfusion bioreactor enabled fluid-derived shear stress conditions for novel bone metastatic prostate cancer testbed.

Metastatic prostate cancer spreads preferentially to the bone, causing skeletal complications associated with significant morbidity and a poor prognosis, despite current therapeutic approaches. Hence, it is imperative to understand the complex metastatic cascade to develop therapeutic interventions for treating metastatic prostate cancer. Increasing evidence suggests the synergistic role of biochemical and biophysical cues in cancer progression at metastases. However, the mechanism underlying the crosstalk between interstitial flow-induced mechanical stimuli and prostate cancer progression at the bone microenvironment remains poorly understood. To this end, we have developed a three-dimensional (3D)in vitrodynamic model of prostate cancer bone metastasis using perfusion bioreactor and compared our results with static conditions to delineate the role of flow-induced shear stress on prostate cancer progression at metastases. We observed an increase in human mesenchymal stem cell (hMSCs) proliferation and differentiation rate under the dynamic culture. The hMSCs form cell agglutinates under static culture, whereas the hMSCs exhibited a directional alignment with broad and flattened morphology under dynamic culture. Further, the expression of mesenchymal to epithelial transition biomarkers is increased in bone metastasized prostate cancer models, and large changes are observed in the cellular and tumoroid morphologies under dynamic culture. Evaluation of cell adhesion proteins indicated that the altered cancer cell morphologies resulted from the constant force pulling due to increased E-cadherin and phosphorylated focal adhesion kinase proteins under shear stress. Overall, we report a successful 3Din vitrodynamic model to recapitulate bone metastatic prostate cancer behavior under dynamic conditions.

Mechanobiological evaluation of prostate cancer metastasis to bone using an in vitro prostate cancer testbed.

Prostate cancer exhibits a propensity to metastasize to the bone, which often leads to fatality. Bone metastasis is characterized by complex biochemical, morphological, pathophysiological, and genetic changes to cancer cells as they colonize at bone sites. In this study, we report the evaluation of MDA PCa2b prostate cancer cells' nanomechanical properties during the mesenchymal-to-epithelial transition (MET) and during disease progression at the metastatic site. Bone-mimetic tissue-engineered 3D nanoclay scaffolds have been used to create in vitro metastatic site for prostate cancer. A significant softening of the prostate cancer cells during MET and further softening as disease progression occurs at metastasis is also reported. The significant reduction in elastic modulus of prostate cancer cells during MET was attributed to actin reorganization and depolymerization. This study provides input towards direct nanomechanical measurements to evaluate the time evolution of cells' mechanical behavior in tumors at bone metastasis site.

Compression of Na-Montmorillonite Swelling Clay Interlayer Is Influenced by Fluid Polarity: A Steered Molecular Dynamics Study.

The compressive responses of an interlayer of the dry sodium-montmorillonite (Na-MMT) swelling clay as well as the clay intercalated with organic fluids of a wide range of dielectric constants from 110 (formamide) to 20 (acetone) are quantitatively evaluated using steered molecular dynamics simulations. Representative dry clay and clay with fluid (clay-fluid) molecular models are constructed, and the stress-strain relationships upon compression of these models are studied using constant force steered molecular dynamics (SMD) simulations. Our results show that the polarity of the fluids and the amount of the fluid molecules in the clay interlayer play a significant role in the interlayer spacing, interlayer volume, interlayer strain, interlayer modulus, nonbonded interactions, and conformation of the fluid molecules upon externally applied stresses. The clay interlayer responses upon compression are essential for the development of multiscale modeling of swelling clays and prediction of the reliable compressive behavior, which are critical for the accurate analysis and economical design of the infrastructures in swelling clay areas and the densification of clays for ceramics manufacturing.

Bone interface modulates drug resistance in breast cancer bone metastasis.

Metastatic breast cancer cells on arriving at bone site interact with the bone cells to influence their growth, proliferation, and chemoresistance. There are currently no effective therapeutics available in the clinic for bone metastases. Many existing anti-cancer therapeutics are ineffective at the metastatic bone site due to a lack of accurate models of breast cancer bone metastasis for drug screening. Here, we report the development of an effective in vitro model using osteogenically differentiated human mesenchymal stem cells (MSCs) and human breast cancer cells on 3D nanoclay scaffolds as a testbed for screening drugs. Our results demonstrate that breast cancer cells grown in 3D bone-mimetic scaffolds exhibited altered physiological and biochemical properties, including tumoroids formation, elevated levels of cytokine such as IL-6, and its downstream effector-mediated inhibition of apoptosis and upregulation of multidrug transporters proteins, leading to drug resistance against paclitaxel. Most importantly, Signal Transducer and Activator of Transcription 3 (STAT3), a potential biomarker for chemoresistance in many cancers, was activated in the 3D breast cancer bone metastasis model. Thus, our data suggest that 3D bone-mimetic nanoclay scaffolds-based in vitro tumor model is a promising testbed for screening new therapeutics for breast cancer bone metastasis where bone interface governs drug resistance in breast cancer cells.

Prostate Cancer Phenotype Influences Bone Mineralization at Metastasis: A Study Using an In Vitro Prostate Cancer Metastasis Testbed.

In this study, two types of prostate cancer cell lines, highly metastatic PC-3 and low metastatic MDA PCa 2b (PCa) were cultured on bone mimetic scaffolds to recapitulate metastasis to bone. A unique in vitro 3D tumor model that uses a sequential culture (SC) of human mesenchymal stem cells followed by seeding with cancer cells after bone formation was initiated to study the phenotype-specific interaction between prostate cancer cells and bone microenvironment. The PCa cells were observed to be less prolific and less metastatic, and to form multicellular tumoroids in the bone microenvironment, whereas PC-3 cells were more prolific and were highly metastatic, and did not form multicellular tumoroids in the bone microenvironment. The metastatic process exhibited by these two prostate cancer cell lines showed a significant and different effect on bone mineralization and extracellular matrix formation. Excessive bone formation in the presence of PC-3 and significant osteolysis in the presence of PCa were observed, which was also indicated by osteocalcin and MMP-9 expression as measured by ELISA and qRT-PCR. The field emission scanning electron microscopy images revealed that the structure of mineralized collagen in the presence of PC-3 is different than the one observed in healthy bone. All experimental results indicated that both osteolytic and osteoblastic bone lesions can be recapitulated in our tumor testbed model and that different cancer phenotypes have a very different influence on bone at metastasis. The 3D in vitro model presented in this study provides an improved, reproducible, and controllable system that is a useful tool to elucidate osteotropism of prostate cancer cells. © 2019 The Authors. JBMR Plus published by Wiley Periodicals, Inc. on behalf of American Society for Bone and Mineral Research.

Wnt/ß-Catenin Signaling Pathway Regulates Osteogenesis for Breast Cancer Bone Metastasis: Experiments in an In Vitro Nanoclay Scaffold Cancer Testbed.

Breast cancer shows a high affinity toward bone, causing bone-related complications, leading to a poor clinical prognosis. The Wnt/ß-catenin signaling pathway has been well-documented for the bone regenerative process; however, the regulation of the Wnt/ß-catenin pathway in breast cancer bone metastasis is poorly explored. Here, we report that the Wnt/ß-catenin signaling pathway has a significant effect on osteogenesis during breast cancer bone metastasis. In this study, we have created a 3D in vitro breast cancer bone metastatic microenvironment using nanoclay-based scaffolds along with osteogenically differentiated human mesenchymal stem cells (MSCs) and human breast cancer cells (MCF-7 and MDA-MB-231). The results showed upregulation in expressions of Wnt-related factors (Wnt-5a, ß-catenin, AXIN2, and LRP5) in sequential cultures of MSCs with MCF-7 as compared to sequential cultures of MSCs with MDA-MB-231. Sequential cultures of MSCs with MCF-7 also showed higher ß-catenin expression on the protein levels than sequential cultures of MSCs with MDA-MB-231. Stimulation of Wnt/ß-catenin signaling in sequential cultures of MSCs with MCF-7 by ET-1 resulted in increased bone formation, whereas inactivation of Wnt/ß-catenin signaling by DKK-1 displayed a significant decrease in bone formation, mimicking bone lesions in breast cancer patients. These data collectively demonstrate that Wnt/ß-catenin signaling governs osteogenesis within the tumor-harboring bone microenvironment, leading to bone metastasis. The nanoclay scaffold provides a unique testbed approach for analysis of the pathways of cancer metastasis.

Fourier transform infrared spectroscopy based spectral biomarkers of metastasized breast cancer progression.

Breast cancer is a global health issue and the second leading cause of cancer death in women. Breast cancer tends to migrate to bone and causes bone metastases which is ultimately the cause of death. Here, we report the use of FTIR to identify spectral biomarkers of cancer progression on 3D in vitro model of breast cancer bone metastasis. Our results indicate that the following spectral biomarkers can monitor cancer progression, for example, lipids (CH2 asymmetric/CH2 symmetric stretch), Amide I/Amide II, and RNA/DNA. Principal component analysis also confirmed the involvement of protein, lipids and nucleic acids in cancer progression on sequential culture. The collective observations from this study suggest successful application of FTIR as a non-invasive and accurate method to identify biochemical changes in cancer cells during the progression of breast cancer bone metastasis.