Coarse-grained System Research Articles

Cross-correlation corrected friction in generalized Langevin models: Application to the continuous Asakura-Oosawa model.

The development of dynamically consistent coarse-grained models for molecular simulations is often based on generalized Langevin equations, motivated by the application of the projection operator formalism (Mori-Zwanzig theory). While Mori's projection operator yields linear generalized Langevin equations that can be computationally efficiently implemented in numerical simulations, the downside is that Mori's generalized Langevin equation does not encompass the multi-body potential of mean force required to correctly encode structural and thermodynamic properties in coarse-grained many-body systems. Zwanzig's projection operator yields nonlinear generalized Langevin equations including the multi-body potential of mean force, while the remaining force contributions are not as cheap to implement in molecular simulation without making it formally hard to justify approximations. For many-particle coarse-grained models, due to computational and conceptual simplicity, an often used approach is to combine nonlinear conservative interactions with linear expressions to model dissipation. In a previous study [V. Klippenstein and N. F. A. van der Vegt, J. Chem. Phys. 154, 191102 (2021)], we proposed a method to parameterize such models to achieve dynamic consistency in coarse-grained models, allowing us to reconcile Mori's and Zwanzig's approach for practical purposes. In the current study, by applying the same strategy, we develop coarse-grained implicit solvent models for the continuous Asakura-Oosawa model, which under certain conditions allows us to develop very accurate coarse-grained potentials. By developing coarse-grained models for different reference systems with varying parameters, we test the broader applicability of the proposed procedure and demonstrate the relevance of accurate coarse-grained potentials in bottom-up derived dissipative models. We study how different system parameters affect the dynamic representability of the coarse-grained models. In particular, we find that the quality of the coarse-grained potential is crucial to correctly model the backscattering effect due to collisions on the coarse-grained scale. As hydrodynamic interactions are not explicitly modeled in the presented coarse-graining approach, deviations are observed in the long-time dynamics. The Asakura-Oosawa model allows for the tuning of system parameters to gain an improved understanding of this limitation. We also propose three new iterative optimization schemes to fine-tune the generalized Langevin thermostat to exactly match the reference velocity-autocorrelation function.

Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework.

The appeal of multiscale modeling approaches is predicated on the promise of combinatorial synergy. However, this promise can only be realized when distinct scales are combined with reciprocal consistency. Here, we consider multiscale molecular dynamics (MD) simulations that combine the accuracy and macromolecular flexibility accessible to fixed-charge all-atom (AA) representations with the sampling speed accessible to reductive, coarse-grained (CG) representations. AA-to-CG conversions are relatively straightforward because deterministic routines with unique outcomes are achievable. Conversely, CG-to-AA conversions have many solutions due to a surge in the number of degrees of freedom. While automated tools for biomolecular CG-to-AA transformation exist, we find that one popular option, called Backward, is prone to stochastic failure and the AA models that it does generate frequently have compromised protein structure and incorrect stereochemistry. Although these shortcomings can likely be circumvented by human intervention in isolated instances, automated multiscale coupling requires reliable and robust scale conversion. Here, we detail an extension to Multiscale Machine-learned Modeling Infrastructure (MuMMI), including an improved CG-to-AA conversion tool called sinceCG. This tool is reliable (∼98% weakly correlated repeat success rate), automatable (no unrecoverable hangs), and yields AA models that generally preserve protein secondary structure and maintain correct stereochemistry. We describe how the MuMMI framework identifies CG system configurations of interest, converts them to AA representations, and simulates them at the AA scale while on-the-fly analyses provide feedback to update CG parameters. Application to systems containing the peripheral membrane protein RAS and proximal components of RAF kinase on complex eight-component lipid bilayers with ∼1.5 million atoms is discussed in the context of MuMMI.

Development of coarse-grained potential of silica species

ABSTRACT Understanding the molecular transformation of silica aggregates during silica polymerisation is crucial to control the properties of final products such as zeolite, nanoparticles, mesoporous silica and other polymorphs. Nevertheless, molecular events during synthesis are challenging to probe using experimental techniques. Computational tools are beneficial to probe molecular length and time scales; however, the complex systems with significant degrees of freedom require significant computational resources. In this work, we have developed coarse-grained (CG) potentials for silica system wherein every silica tetrahedron (Si(OH)O) having ‘z’ number of bridging oxygen is mapped to a unique CG silica bead (). Different composition of these CG silica beads represent a polymerised silica system with varying degrees of condensation. We performed molecular dynamics (MD) simulations of all-atom silica system to obtain reference radial distribution functions between various silica species (), which was used in Monte Carlo simulations of the CG system to obtain CG potentials. We iteratively refined the CG potentials using iterative Boltzmann inversion and inverse Monte Carlo techniques. We found two attractive minima in the CG potential between arising due to direct and indirect interactions of species representing first and second coordination shells. The strength of CG potential increases for both of minima with increasing number of bridging oxygen in species. We performed MD simulations of CG silica beads using developed CG potentials at two degree of condensations and found equilibrium structure of spherical silica nanoparticle. We found that and species are predominantly located at the centre of nanoparticles, whereas species are present uniformly.

Multiscale Simulation of Ternary Stratum Corneum Lipid Mixtures: Effects of Cholesterol Composition.

Molecular dynamics simulations of mixtures of the ceramide nonhydroxy-sphingosine (NS), cholesterol, and a free fatty acid are performed to gain molecular-level understanding of the structure of the lipids found in the stratum corneum layer of skin. A new coarse-grained force field for cholesterol was developed using the multistate iterative Boltzmann inversion (MS-IBI) method. The coarse-grained cholesterol force field is compatible with previously developed coarse-grained force fields for ceramide NS, free fatty acids, and water and validated against atomistic simulations of these lipids using the CHARMM force field. Self-assembly simulations of multilayer structures using these coarse-grained force fields are performed, revealing that a large fraction of the ceramides adopt extended conformations, which cannot occur in the single bilayer in water structures typically studied using molecular simulation. Cholesterol fluidizes the membrane by promoting packing defects, and an increase in cholesterol content is found to reduce the bilayer thickness due to an increase in interdigitation of the C24 lipid tails, consistent with experimental observations. Using a reverse-mapping procedure, a self-assembled coarse-grained multilayer system is used to construct an equivalent structure with atomistic resolution. Simulations of this atomistic structure are found to closely agree with experimentally derived neutron scattering length density profiles. Significant interlayer hydrogen bonding is observed in the inner layers of the atomistic multilayer structure that are not found in the outer layers in contact with water or in equivalent bilayer structures. This work highlights the importance of simulating multilayer structures, as compared to the more commonly studied bilayer systems, to enable more appropriate comparisons with multilayer experimental membranes. These results also provide validation of the efficacy of the MS-IBI derived coarse-grained force fields and the framework for multiscale simulation.

Generalized Langevin equationwith a nonlinear potential of mean force and nonlinear memory friction from a hybrid projection scheme.

We introduce a hybrid projection scheme that combines linear Mori projection and conditional Zwanzig projection techniques and use it to derive a generalized Langevin equation(GLE) for a general interacting many-body system. The resulting GLE includes (i) explicitly the potential of mean force (PMF) that describes the equilibrium distribution of the system in the chosen space of reaction coordinates, (ii) a random force term that explicitly depends on the initial state of the system, and (iii) a memory friction contribution that splits into two parts: a part that is linear in the past reaction-coordinate velocity and a part that is in general nonlinear in the past reaction coordinates but does not depend on velocities. Our hybrid scheme thus combines all desirable properties of the Zwanzig and Mori projection schemes. The nonlinear memory friction contribution is shown to be related to correlations between the reaction-coordinate velocity and the random force. We present a numerical method to compute all parameters of our GLE, in particular the nonlinear memory friction function and the random force distribution, from a trajectory in reaction coordinate space. We apply our method on the dihedral-angle dynamics of a butane molecule in water obtained from atomistic molecular dynamics simulations. For this example, we demonstrate that nonlinear memory friction is present and that the random force exhibits significant non-Gaussian corrections. We also present the derivation of the GLE for multidimensional reaction coordinates that are general functions of all positions in the phase-space of the underlying many-body system; this corresponds to a systematic coarse-graining procedure that preserves not only the correct equilibrium behavior but also the correct dynamics of the coarse-grained system.

Design and Implementation of a Dynamic Task Mapping Algorithm Based on Hotspot Statistics

In a coarse-grained heterogeneous multi-core system, the task map is responsible for allocating the cores for task execution. The existing user static mapping method has low programming friendliness. As the scale and density of system tasks increase, so does the complexity of manual programming by users, resulting in programming inefficiencies. Aiming at this problem, based on the existing heterogeneous multi-core platform, this paper studies a dynamic task mapping method with hotspot statistics, and uses the preprocessing of the mapping to reduce the time spent on the actual mapping. The hardware mapper is designed and implemented in Verilog, and the verification platform is built in the HDL environment. The experimental results show that the new mapping algorithm significantly improves the performance of the system, with an average of 32.50% and a maximum of 47.16%.

Elucidating the role of network topology dynamics on the coil-stretch transition hysteresis in extensional flow of entangled polymer melts

Dissipative particle dynamics (DPD) simulations are performed on coarse-grained replicas of linear, monodisperse entangled polyethylene melts C1000H2002 and C3000H6002 undergoing both steady-state and transient planar elongational flow (PEF). The fidelity of the DPD simulations is verified by direct comparison of flow topological and rheological properties of a 334-particle chain liquid against the united-atom C1000H2002 liquid, simulated using nonequilibrium molecular dynamics (NEMD). These DPD simulations demonstrate that a flow-induced coil-stretch transition (CST) and its associated hysteresis caused by configurational microphase separation, as observed in previous NEMD simulations of PEF, can be replicated using a more computationally efficient coarse-grained system. Results indicate that the breadth of the CST hysteresis loop is enlarged for the longer molecule liquid relative to the shorter one. Furthermore, relaxation simulations reveal that reducing the applied flow Deborah number (De) from a high value corresponding to a homogeneous phase of highly stretched molecules to a De within the biphasic region results in a two-stage relaxation process. There is a fast initial stratification of the kinetically trapped highly stretched chains into regions of highly extended and less extended chains, which displays similar behavior to a system undergoing a spinodal decomposition caused by spatial configurational free energy fluctuations. After a short induction period of apparently random duration, the less extended chain regions experience a stochastic nucleation event that induces configurational relaxation to domains composed of coiled molecules over a much longer time scale, leaving the more highly extended chains in surrounding sheetlike domains. The time scales of these two relaxation processes are of the same order of magnitude as the Rouse and disengagement times of the equilibrium liquids.

Coarse-Grained Dynamically Accurate Simulations of Ionic Liquids: [pyr14][TFSI] and [EMIM][BF4

In this work, coarse-grained (CG) models for two different sets of ionic liquids were developed from atomistic molecular dynamics (MD) reference systems, expanding their system size and time duration capabilities. The bonded force field of the CG systems was built using harmonic oscillator potential (HOP) fitting, while the nonbonded force field was generated with the multiscale coarse-graining (MS-CG) approach based on force matching. The dynamics of each system were corrected using the probability distribution function-based coarse-grained molecular dynamics (PDF-based CGMD) method. The structure and dynamics of each system were proven to match reference system data at two temperature scales. CG models and force fields for these liquids were developed to exemplify a general purpose methodology for producing MD results of ionic liquids and other fluids with accurate structural as well as dynamic properties. As an application, developed ionic liquids CG models were then applied to study vacuum-interface interaction. Density profile results of vacuum-interface exposure show significant deviation from bulk behavior. At the interface, multilayer ordering of ionic liquids is predicted to be similar to those observed from an experimental work. This ordering is intensified by decreasing temperature and use of the PDF-based CGMD method as opposed to conventional CG methods.

Evaluation of Interactions between SARS-CoV-2 RBD and Full-Length ACE2 with Coarse-Grained Molecular Dynamics Simulations.

Compared to all-atom models, coarse-grained models enable the investigation of the dynamics of simulation systems on a much larger length scale and a longer time scale, which makes them suitable for studying macromolecular systems. Hence, in this work, we performed multiple μs-scale Martini coarse-grained molecular dynamics simulations to reveal the interaction details between SARS-CoV-2 RBD and full-length human ACE2. Besides, the key coarse-grained systems were backmapped into the corresponding all-atom system for the display of structural details. Our results indicated that the plier structure in two ends of the binding interface plays a key role in the binding process of SARS-CoV-2 RBD with ACE2. Furthermore, we also found that when there is no B0AT1 in the simulation system, the N-terminus of ACE2 is more likely to approach the cell membrane, which has a strong correlation with the subsequent fusion of the virus with the cell membrane. These binding details of SARS-CoV-2 RBD and the ACE2 protease domain (PD) as well as the membrane orientation thermodynamics can promote the development of therapeutic drugs and preventive vaccines against SARS-CoV-2.

Mathematical Framework for Breathing Chimera States

About two decades ago it was discovered that systems of nonlocally coupled oscillators can exhibit unusual symmetry-breaking patterns composed of coherent and incoherent regions. Since then such patterns, called chimera states, have been the subject of intensive study but mostly in the stationary case when the coarse-grained system dynamics remains unchanged over time. Nonstationary coherence–incoherence patterns, in particular periodically breathing chimera states, were also reported, however not investigated systematically because of their complexity. In this paper we suggest a semi-analytic solution to the above problem providing a mathematical framework for the analysis of breathing chimera states in a ring of nonlocally coupled phase oscillators. Our approach relies on the consideration of an integro-differential equation describing the long-term coarse-grained dynamics of the oscillator system. For this equation we specify a class of solutions relevant to breathing chimera states. We derive a self-consistency equation for these solutions and carry out their stability analysis. We show that our approach correctly predicts macroscopic features of breathing chimera states. Moreover, we point out its potential application to other models which can be studied using the Ott–Antonsen reduction technique.

The Bak core dimer focuses triacylglycerides in the membrane

Apoptosis, the intrinsic programmed cell death process, is mediated by the Bcl-2 family members Bak and Bax. Activation via formation of symmetric core dimers and oligomerization on the mitochondrial outer membrane (MOM) leads to permeabilization and cell death. Although this process is linked to the MOM, the role of the membrane in facilitating such pores is poorly understood. We recently described Bak core domain dimers, revealing lipid binding sites and an initial role of lipids in oligomerization. Here we describe simulations that identified localized clustering and interaction of triacylglycerides (TAGs) with a minimized Bak dimer construct. Coalescence of TAGs occurred beneath this Bak dimer, mitigating dimer-induced local membrane thinning and curvature in representative coarse-grain MOM and model membrane systems. Furthermore, the effects observed as a result of coarse-grain TAG cluster formation was concentration dependent, scaling from low physiological MOM concentrations to those found in other organelles. We find that increasing the TAG concentration in liposomes mimicking the MOM decreased the ability of activated Bak to permeabilize these liposomes. These results suggest that the presence of TAGs within a Bak-lipid membrane preserves membrane integrity and is associated with reduced membrane stress, suggesting a possible role of TAGs in Bak-mediated apoptosis.

Investigation of Crystallization and Relaxation Effects in Coarse-Grained Polyethylene Systems after Uniaxial Stretching.

In this study, we investigate the thermo-mechanical relaxation and crystallization behavior of polyethylene using mesoscale molecular dynamics simulations. Our models specifically mimic constraints that occur in real-life polymer processing: After strong uniaxial stretching of the melt, we quench and release the polymer chains at different loading conditions. These conditions allow for free or hindered shrinkage, respectively. We present the shrinkage and swelling behavior as well as the crystallization kinetics over up to 600 ns simulation time. We are able to precisely evaluate how the interplay of chain length, temperature, local entanglements and orientation of chain segments influences crystallization and relaxation behavior. From our models, we determine the temperature dependent crystallization rate of polyethylene, including crystallization onset temperature.

Coarse-grained meandering distributive fluvial system of the basal Cedar Mountain Formation, U.S.A.

ABSTRACT The analysis of downstream changes in ancient fluvial systems can better inform depositional models for foreland-basin systems. Herein we analyze the basal deposits of the Early Cretaceous Cedar Mountain Formation of Utah to better understand the variety of fluvial deposits present and to develop a depositional model for the Sevier foreland basin. We also evaluate the long-held interpretation of a braided origin for these deposits and document numerous examples of point-bar deposition in highly sinuous meandering rivers by analysis of large (20 to 60 km2) plan-view exposures. These plan-view exposures allow comparisons between planform and cross-sectional geometries. The study utilizes outcrop data, virtual outcrop models, and satellite imagery to develop a facies model and analyze the architecture of channel bodies in the Buckhorn Conglomerate and Poison Strip Sandstone of the Cedar Mountain Formation. We document downstream (west to east) decreases in lateral channel migration, sinuosity, channel amalgamation, grain size, and percent of fluvial channel facies (conglomerate and sandstone). Fluvial channel deposits occur arranged into larger stratal bodies: multistory–multilateral channel bodies that are dominantly composed of clast-supported conglomerate in the west to a mix of multistory, multilateral, and isolated channel bodies composed of matrix-supported conglomerate in the east. The median width of highly sinuous point bars is similar across the field area (344 m to 477 m), but the inclusion of narrower (median = 174 m), low-sinuosity bar elements in the east indicates an overall reduction in lateral channel migration and sinuosity downstream. Net-to-gross values range from 100% in much of the western outcrops to as low as 38% in the east. Paleocurrent analysis reveals a transverse (west to east) paleoflow for the study interval that merges with axial (south–north) paleoflow near the Utah–Colorado state line. We estimate 104 m3/s-scale discharge and 106 kilometer-scale drainage area for axial rivers based on paleohydraulic analysis which represents a significant part of the Early Cretaceous continental-scale drainage. The observed downstream trends in lateral channel migration, sinuosity, channel amalgamation, grain size, and net-to-gross for the basal Cedar Mountain Formation are consistent with expected trends for sinuous single-thread distributive fluvial systems and are similar to observed trends in the Jurassic Morrison Formation. Medial (Buckhorn Conglomerate) to distal (Poison Strip Sandstone) zones are preserved and span the forebulge to backbulge depozones of a foreland-basin system. Postulated deposits of the proximal distributive fluvial system have been removed during erosion of the foredeep depozone. The easternmost Poison Strip Sandstone and coeval Burro Canyon Formation represent deposits of an axial system at which western-sourced distributive fluvial systems end. Distributive fluvial systems dominate modern foreland basins, and this study suggests that they may constitute a significant proportion of ancient successions.

EDP-convergence for a linear reaction-diffusion system with fast reversible reaction

We perform a fast-reaction limit for a linear reaction-diffusion system consisting of two diffusion equations coupled by a linear reaction. We understand the linear reaction-diffusion system as a gradient flow of the free energy in the space of probability measures equipped with a geometric structure, which contains the Wasserstein metric for the diffusion part and cosh-type functions for the reaction part. The fast-reaction limit is done on the level of the gradient structure by proving EDP-convergence with tilting. The limit gradient system induces a diffusion system with Lagrange multipliers on the linear slow-manifold. Moreover, the limit gradient system can be equivalently described by a coarse-grained gradient system, which induces a diffusion equation with a mixed diffusion constant for the coarse-grained slow variable.

Entanglement Renormalization of Thermofield Double States.

Entanglement renormalization is a method for "coarse graining" a quantum state in real space, with the multiscale entanglement renormalization ansatz as a notable example. We obtain an entanglement renormalization scheme for finite-temperature (Gibbs) states by applying the multiscale entanglement renormalization ansatz to their canonical purification, the thermofield double state. As an example, we find an analytically exact renormalization circuit for a finite-temperature two-dimensional toric code that maps it to a coarse-grained system with a renormalized higher temperature, thus explicitly demonstrating its lack of topological order. Furthermore, we apply this scheme to one-dimensional free boson models at a finite temperature and find that the thermofield double corresponding to the critical thermal state is described by a Lifshitz theory. We numerically demonstrate the relevance and irrelevance of various perturbations under real space renormalization.

A coarse-grained – Atomistic multi-scale method to study the mechanical behavior of heterogeneous FCC nano-materials

In this paper, a multi-scale method is developed to couple the atomistic domain with the coarse-grained system to model the mechanical properties of materials with defects and heterogeneity. The material properties are determined in the nano-scale level by Molecular Dynamics analysis, in which the interatomic potential is used to determine the interaction between the particles. The main issue with the Molecular Dynamics method is its high computational cost. Hence, the coarse-grained method is employed, where a number of atoms are assumed as a bigger bid, and the interatomic potential is modified in terms of the position of the grains. This method reduces the computational cost as the degrees of freedom decreases. Moreover, it has the advantage of using the same interatomic potential as molecular dynamics method comparing to the continuum-based approaches. One issue with the coarse-grained method is that phenomena with small wavelengths cannot be captured comparing to the all-atoms system. To this end, a multi-scale method is presented to couple the atomistic domain with the coarse-grained system. In this method, the regions near to the cracks, defects, or heterogeneity are modeled by the conventional MD scheme and farther regions by the coarse-grained method. In order to illustrate the capability of the proposed computational model, the evolution of misfit dislocation is investigated at the interface of Ni3Aland Ni, which is formed by their subtle difference in lattice parameter. Obviously, dislocations play a crucial role in determining the mechanical behavior of superalloys even though a considerable number of atoms are located in perfect lattice-structures, and dislocations comprise a small region of the domain. Thus, it is rational to apply the proposed CG–MD multi-scale method to study the mechanical behavior of such materials. Finally, the effect of loading and temperature is investigated on dislocation density of the Ni-based superalloys using the CG–MD multi-scale method; it is shown that dislocation density increases as the temperature or strain increases.

Nonuniqueness of fluctuating momentum in coarse-grained systems.

Coarse-grained descriptions of microscopic systems often require a mesoscopic definition of momentum. The question arises as to the uniqueness of such a momentum definition at a particular coarse-graining scale. We show here that particularly the fluctuating properties of common definitions of momentum in coarse-grained methods like lattice gas and lattice Boltzmann do not agree with a fundamental definition of momentum. In the case of lattice gases, the definition of momentum will even disagree in the limit of large wavelength. For short times we derive analytical representations for the distribution of different momentum measures and thereby give a full account of these differences.

Effects of Trehalose on Lipid Membranes under Rapid Cooling using All-Atom and Coarse-Grained Molecular Simulations.

We investigate the effect of the cryopreservative α-α-trehalose on a model 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipid membrane undergoing cooling from 350 to 250 K using all-atom (AA) and coarse-grained (CG) molecular dynamics simulation. In the AA simulations, we find that the addition of trehalose alters the Lα (liquid crystalline) to Pβ (ripple) phase transition, suppressing the major domain of the Pβ phase and increasing the degree of leaflet interdigitation (the minor domain) which yields a thinner membrane with a higher area per lipid. Calculation of dihedral angle distributions for the lipid tails shows a greater fraction of gauche angles in the Pβ phase as trehalose concentration is increased, indicating that trehalose increases lipid disorder in the membrane. In contrast, the CG simulations transition directly from the Lα to the Lβ (gel) phase upon cooling without exhibiting the Pβ phase (likely due to increased lipid mobility in the CG system). Even so, the CG simulations show that the addition of trehalose clearly suppresses the Lα to Lβ phase transition, demonstrating that trehalose increases lipid disorder at low temperatures for the CG system, similar to the AA. Analysis using a two-state binding model provides net affinity coefficients between trehalose and the membrane as well as trehalose partition coefficients between the membrane interface and the bulk solution for both the AA and CG systems.

Complex stratigraphic fill of a small, confined syn-rift basins: an Upper Jurassic example from offshore mid-Norway

Abstract Extensional rift basin systems have been a focus of study for hydrocarbon exploration and have provided significant economic reserves in recent decades, which has led to advances in our understanding of their tectono-sedimentary evolution. However, with the increasing maturity of such settings, focus is shifting from pre-rift structures to the underexplored syn- and late-rift plays. This change in focus brings with it a significant increase in complexity when trying to develop an integrated understanding of the sedimentological, sequence stratigraphic and structural conditions that control the distribution of syn-rift reservoirs. Here we present a subsurface example from offshore Norway of a small, confined, syn-tectonic basin sourced from a local basement high. 3D seismic data, sedimentary facies analysis and stratigraphic correlations based on well and core data from six key wells constrain the local and regional tectonic controls. The PL586 licence partners drilled several wells between 2014 and 2015 targeting syn-rift Upper Jurassic stratigraphy on the southern Halten Terrace. The wells penetrated a complete syn-rift stratigraphic sequence, which provided an excellent subsurface record of the inherent complexities encountered in small, confined (3 by 5 km) syn-rift basins. Seismic data reveals that the Late Jurassic hanging-wall basin architecture and the footwall hinterland of the Frøya High were controlled by activity on the basin-bounding Vingleia Fault Complex. Facies analysis from well and core data reflects a complete syn-rift succession. The early-rift succession comprises mainly mud and siltstone with minor fine-grained sandstones interpreted to be deposited by sediment gravity flows in isolated mini-basins. The peak-rift deposits comprise coarse-grained sediment gravity flows that were sourced locally from the uplifting footwall and deposited as coarse-grained submarine fan systems in the immediate hanging wall. Significant footwall uplift during the peak-rift phase resulted in fault scarp instability and the emplacement of several large landslide complexes into the basin. The late-rift phase is dominated by a mud-rich sequence with minor coarse-grained apron fans shedding sediment off the basin bounding fault and shoreface deposits flanking the hanging-wall dip-slope and subtle intra-basinal highs. This subsurface study from the southern Halten Terrace is significant in the number of wells that have specifically targeted syn-rift stratigraphy and the level of detail at which it captures the stratigraphic variability of these deposits within a small, confined basin system. Integration of seismic geomorphology and well data with robust provenance, dating and stratigraphic correlation has enabled the development of a tectono-stratigraphic model specific to the scale and local tectonic setting. The model reveals that structural evolution ultimately controlled the development of sediment supply routes, their age and distribution, and allows several conclusions to be drawn: The stratigraphy of small, confined syn-rift basins is broadly comparable with more typically documented larger syn-rift settings, although lateral facies changes occur more rapidly. The cannibalistic nature of syn-rift systems, where a large volume of pre- and syn-rift sediments are uplifted and eroded then rapidly re-deposited makes determining the relative age of laterally variable depositional settings difficult. In order to adequately constrain the timing and depositional extent of syn-rift stratigraphy, it is essential to understand the structural evolution of the system and integrate this information with other disciplines and datasets. This integrated understanding will ultimately improve predictions of reservoir presence and quality.

Polyphase extensional basins: interplay between tectonics and sedimentation in the Neogene Siena-Radicofani Basin (Northern Apennines, Italy)

Rift-basins are the shallow effects of lithosphere-scale extensional processes often producing polyphase faulting. Their sedimentary evolution depends on the mutual interplay between tectonics, climate, and eustasy. Estimating the role of each factor is generally a challenging issue. This paper is focused on the tectono-sedimentary evolution of the Neogene Siena-Radicofani Basin, a polyphase structural depression located in the inner Northern Apennines. Since Miocene, this basin developed after prolonged extensional tectonics, first as a bowl-shaped structural depression, later reorganized into a half-graben structure due to the activation of high-angle normal faults in the Zanclean. At that time the basin contained coeval continental and marine settings controlled by the normal faulting that caused the development of local coarse-grained depositional systems. These were investigated to: (i) discriminate between the influences of tectonics and climate on sedimentation patterns, and (ii) provide detailed time constraints on fault activity. The analysed successions were deposited in an interval between 5.08 and 4.52 Ma, when a climate-induced highstand phase occurred throughout the Mediterranean. However, evidence of local relative sea-level drops is registered in the sedimentary record, often associated with increased accommodation space and sediment supply. Such base-level fluctuations are not connected to climate changes, suggesting that the faults generally control sedimentation along the basin margins.