Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.64898/2026.01.03.697499

LignAmb25: A Comprehensive AMBER Force Field Addressing Lignin's Structural and Chemical Diversity

Lapsien, M.·Bonus, M.·Greb, J.·Gohlke, H.
View original source ↗Export metadata ↓

Abstract

LignAmb25 is a comprehensive force field for lignin molecular dynamics simulations implemented natively within the AMBER package. The force field includes parameters for all common monolignol units (p-coumaryl, coniferyl, caffeyl, and sinapyl alcohol) and their associated linkages ({beta}-O4, {beta}-5, {beta}-{beta}, {beta}-1, 5-5, 5-O4, -O4, BDO, and DBDO), along with less commonly encountered units such as tricin, spirodienones, and hydroxystilbenes. This enables simulations of both softwood and hardwood lignin structures with compositions that would be difficult to isolate experimentally. Force field parameters were initially derived from the GAFF2 force field and systematically optimized using quantum mechanical calculations at the {omega}B97X-D4/def2-TZVPP level of theory on conformer ensembles derived via the CREST/CENSO conformational sampling toolchain. Partial atomic charges were derived using the RESP methodology, consistent with AMBER conventions. Experimentally measured crystal structures of lignin simulated with LignAmb25 accurately retain their packing based on calculations of the RMSD and density error compared to the deposited crystal structure, thereby exceeding the performance of the lignin force field for CHARMM. Additionally, LignAmb25 is shown to reliably estimate the enthalpy of vaporization and the absolute hydration free energy of lignin-related compounds. The LignAmb25 force field is provided in two variants: LignAmb25Solo, a standalone version not meant for use with other biomolecular force fields that focuses on accurate modelling of lignin-solvent interactions, and LignAmb25HF, a version that is compatible with all other major biomolecular force fields in the AMBER molecular dynamics suite. This includes force fields of the GLYCAM (carbohydrates), ff19SB (proteins), and LIPID (lipids) families, as well as the DNA and RNA force fields routinely used in AMBER. The LignAmb25 force field will be distributed as of AMBER 26. Statement of significanceLignin, a complex aromatic heteropolymer comprising up to 40% of plant biomass, remains one of the most challenging biopolymers to characterize experimentally due to its structural heterogeneity, recalcitrance against depolymerization and selective chemical conversion, and lack of a defined primary sequence. Traditional wet-lab analytical methods face significant limitations, including lignins poor solubility, tendency to aggregate, and structural modifications during extraction and analysis. These experimental challenges make computational approaches essential for understanding the molecular basis of lignins physicochemical properties and for advancing lignocellulosic biomaterial applications. We present LignAmb25, a molecular mechanics force field for lignin implemented within AMBER, enabling researchers to investigate lignin structures and dynamics under conditions difficult to access experimentally. LignAmb25 integrates into the AMBER force field system and represents an alternative to the lignin force field for CHARMM. It improves upon the latter by including spirodienones and hydroxystilbenes as less commonly encountered monolignol units and the addition of several new linkages.

Source connections

Explore related subjects

biophysicsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Lapsien, M., Bonus, M., Greb, J., Gohlke, H.. 2026-01-03. LignAmb25: A Comprehensive AMBER Force Field Addressing Lignin's Structural and Chemical Diversity. https://doi.org/10.64898/2026.01.03.697499

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Lipid Scrambling Amplifies Plasma Membrane Undulations via Anti-Registered Domains Stabilized by Long-Chain Sphingomyelin

Lipid scrambling, which dissipates the transbilayer lipid asymmetry of plasma membranes (PMs), plays an essential role in various large-scale membrane remodeling processes. Although lipid domains have been implicated in these processes, the underlying mechanisms remain poorly understood, owing to the lack of a molecular-level picture of how lipid scrambling reorganizes these domains. Here, using coarse-grained molecular dynamics simulations of asymmetric and fully scrambled PM models, we show that lipid scrambling markedly enhances membrane undulations. We identify two key features of the domain organization underlying this enhancement in the scrambled PM: domain anti-registration, which couples to membrane curvature through a mismatch in preferred curvature between the two leaflets, and scrambling-induced domain enlargement, which permits this curvature to extend over large length scales. Simulations with different sphingomyelin (SM) compositions demonstrate that long-chain SMs stabilize anti-registered domains and the associated membrane curvature. Together, these results suggest a physical mechanism by which lipid scrambling primes the PM for remodeling through the reorganization of lipid domains, with long-chain SMs playing a key role. We also find that the interleaflet domain organization of the scrambled PM model depends strongly on system size, shifting from anti-registration to registration as the simulation box is reduced, and we discuss the origin of this finite-size effect.

biophysics↗
bioRxiv2026

Evaluating speech-like distortion product otoacoustic emissions: a comparison of time- and frequency-domain metrics across three datasets

Speech-like distortion-product otoacoustic emissions (DPOAEs) allow cochlear activity to be measured during the perception of natural, continuous speech and have been used to study attentional effects in the cochlea. The technique is still young, however, and existing studies differ in stimulus design and in the metric used to quantify the emissions, which makes their results difficult to compare. Here, we reanalysed three existing datasets (106 participants, 14 stimulus types) with a common pipeline. We compared six metrics: the band power of the recording, the magnitude-squared coherence (MSC) between the recording and a DPOAE template, and four metrics derived from their complex cross-correlation, namely peak magnitude, signal-to-noise ratio (SNR), peak area and peak width. A separability index quantified how well each metric separated in-ear recordings from out-of-ear control recordings without emissions. Band power, MSC and SNR separated best, with mean separability indices of about 0.9, whereas the peak magnitude performed worst and was inverted for half of the stimulus types. Since band power does not require a DPOAE template, it serves as a sanity check of the setup rather than as evidence for an emission. The MSC was insensitive to the latency of the emission but well suited for comparisons across stimuli, whereas the cross-correlation additionally provided the latency. The emissions differed significantly between the stimulus types of the three datasets, and those below about 700 Hz were measured least reliably. We derive practical recommendations for the analysis and stimulus design of future experiments.

biophysics↗
bioRxiv2026

Overlap of competing voices may mask attentional effects on speech-like distortion product otoacoustic emissions

Whether selective auditory attention modulates the cochlear amplifier through the medial olivocochlear system remains debated. Using speech-like distortion-product otoacoustic emissions (DPOAEs), elicited by waveforms that follow the harmonics of natural speech, we previously found that selectively attending one of two competing talkers reduced the emissions related to the resolved harmonics of the female voice. Here, we attempted to reproduce this effect in a design that separated different frequency regimes and harmonic resolvability. Forty-four participants attended one of two competing talkers, a female and a male voice, presented to one ear, while speech-like DPOAEs related to both voices were recorded from the other ear. Stimuli were derived from resolved and unresolved harmonics in a low-frequency (up to 1.5 kHz) and a transitional (1.5 to 4 kHz) regime, which required pitch-shifting both voices so that their fundamental frequencies were much closer to each other than in the original study. Speech-like DPOAEs emerged for most stimulus types, although they were weak for some and absent for one. Their amplitude, however, did not depend on attention for any stimulus type. Further time-domain metrics showed only isolated attentional effects of opposite direction for two stimulus types, and a frequency-domain metric showed none. A cochlear excitation model suggests that, due to the closely spaced fundamental frequencies of the two voices, the emissions most comparable to the original study presumably arose at cochlear locations shared by both voices, where attention would modulate both voices alike.

biophysics↗