144 research outputs found
Ultrafast energy flow in the wake of solution phase bimolecular reactions
- Author
- AC Moskun
- AE Bragg
- AL Harris
- Andrew J. Orr-Ewing
- CG Elles
- CJ Smallwood
- David R. Glowacki
- DR Glowacki
- DR Glowacki
- DR Glowacki
- DR Glowacki
- FF Crim
- GA Bethardy
- GA Bethardy
- GA Bethardy
- GA Bethardy
- GA Voth
- JC Owrutsky
- Jeremy N. Harvey
- L Turi
- LX Dang
- M Gruebele
- N Nandi
- PL Geissler
- Rebecca A. Rose
- RM Stratt
- SJ Greaves
- Stuart J. Greaves
- T Fonseca
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- 01/01/2011
- Field of study
Quasi-classical trajectory study of the dynamics of the Cl + CH4â HCl + CH3 reaction
- Publication venue
- 'Royal Society of Chemistry (RSC)'
- Publication date
- 01/01/2011
- Field of study
Exploring human-guided strategies for reaction network exploration: Interactive molecular dynamics in virtual reality as a tool for citizen scientists
- Publication venue
- 'AIP Publishing'
- Publication date
- 21/10/2021
- Field of study
The emerging fields of citizen science and gamification reformulate scientific problems as games or puzzles to be solved. Through engaging the wider non-scientific community, significant breakthroughs may be made by analyzing citizen-gathered data. In parallel, recent advances in virtual reality (VR) technology are increasingly being used within a scientific context and the burgeoning field of interactive molecular dynamics in VR (iMD-VR) allows users to interact with dynamical chemistry simulations in real time. Here, we demonstrate the utility of iMD-VR as a medium for gamification of chemistry research tasks. An iMD-VR "game"was designed to encourage users to explore the reactivity of a particular chemical system, and a cohort of 18 participants was recruited to playtest this game as part of a user study. The reaction game encouraged users to experiment with making chemical reactions between a propyne molecule and an OH radical, and "molecular snapshots"from each game session were then compiled and used to map out reaction pathways. The reaction network generated by users was compared to existing literature networks demonstrating that users in VR capture almost all the important reaction pathways. Further comparisons between humans and an algorithmic method for guiding molecular dynamics show that through using citizen science to explore these kinds of chemical problems, new approaches and strategies start to emerge
Design of and initial results from a Highly Instrumented Reactor for Atmospheric Chemistry (HIRAC)
- Author
- Publication venue
- Publication date
- 01/01/2007
- Field of study
QM/MM MD and Free Energy Simulations of G9a-Like Protein (GLP) and Its Mutants: Understanding the Factors that Determine the Product Specificity
- Author
- AD MacKerell
- B Xiao
- B Xiao
- BD Strahl
- BM Turner
- BR Brooks
- C Martin
- CL Brooks
- DA Humphrey W
- DR Glowacki
- E Neria
- Emanuele Paci
- GM Torrie
- H Wu
- HB Guo
- Hong Guo
- JF Couture
- JF Couture
- Jianzhuang Yao
- MJ Field
- P Hu
- P Hu
- P Ricchiuto
- PA Del Rizzo
- Q Cui
- Q Xu
- QF Bai
- R Marmorstein
- RE Collins
- S Kumar
- S Lall
- SD Taverna
- SL Wang
- ST Xu
- T Jenuwein
- WL Jorgensen
- X Zhang
- X Zhang
- X Zhang
- XD Zhang
- Yuzhuo Chu
- YZ Chu
- Publication venue
- Public Library of Science
- Publication date
- 18/05/2012
- Field of study
Certain lysine residues on histone tails could be methylated by protein lysine methyltransferases (PKMTs) using S-adenosyl-L-methionine (AdoMet) as the methyl donor. Since the methylation states of the target lysines play a fundamental role in the regulation of chromatin structure and gene expression, it is important to study the property of PKMTs that allows a specific number of methyl groups (one, two or three) to be added (termed as product specificity). It has been shown that the product specificity of PKMTs may be controlled in part by the existence of specific residues at the active site. One of the best examples is a Phe/Tyr switch found in many PKMTs. Here quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) and free energy simulations are performed on wild type G9a-like protein (GLP) and its F1209Y and Y1124F mutants for understanding the energetic origin of the product specificity and the reasons for the change of product specificity as a result of single-residue mutations at the Phe/Tyr switch as well as other positions. The free energy barriers of the methyl transfer processes calculated from our simulations are consistent with experimental data, supporting the suggestion that the relative free energy barriers may determine, at least in part, the product specificity of PKMTs. The changes of the free energy barriers as a result of the mutations are also discussed based on the structural information obtained from the simulations. The results suggest that the space and active-site interactions around the Δ-amino group of the target lysine available for methyl addition appear to among the key structural factors in controlling the product specificity and activity of PKMTs
The evolution of multiple active site configurations in a designed enzyme
- Author
- A Bhowmick
- A Labas
- A Li
- A Warshel
- A Warshel
- A Warshel
- AN Alexandrova
- Antonio Fernandez-Ramos
- AS Raman
- AV Marenich
- B Hess
- CP Pan
- D PetroviÄ
- D Röthlisberger
- DG Gibson
- DR Glowacki
- E Campbell
- F Hollfelder
- G Bussi
- G Bussi
- G Jiménez-Osés
- G King
- G Kiss
- G Kiss
- GA Tribello
- H Eyring
- H Liu
- HJC Berendsen
- J Marelius
- J Ryckaert
- JK Lassila
- K Lindorff-Larsen
- L Giger
- L Masgrau
- M Döbele
- M Parrinello
- MD Winn
- MHM Olsson
- MJ Abraham
- ML Casey
- MP Frushicheva
- MP Frushicheva
- MP Meyer
- O Khersonsky
- P Emsley
- PA Karplus
- PD Mabbitt
- PDJ Moens
- PR Callis
- PV Afonine
- PV Afonine
- R Blomberg
- R Manetsch
- RB Best
- RT McGibbon
- Schrödinger Release 3.
- U Essmann
- W Kabsch
- WL Jorgensen
- WL Jorgensen
- X Daura
- Y Miao
- ZD Nagel
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- 01/01/2018
- Field of study
Developments in computational chemistry, bioinformatics, and laboratory evolution have facilitated the de novo design and catalytic optimization of enzymes. Besides creating useful catalysts, the generation and iterative improvement of designed enzymes can provide valuable insight into the interplay between the many phenomena that have been suggested to contribute to catalysis. In this work, we follow changes in conformational sampling, electrostatic preorganization, and quantum tunneling along the evolutionary trajectory of a designed Kemp eliminase. We observe that in the Kemp Eliminase KE07, instability of the designed active site leads to the emergence of two additional active site configurations. Evolutionary conformational selection then gradually stabilizes the most efficient configuration, leading to an improved enzyme. This work exemplifies the link between conformational plasticity and evolvability and demonstrates that residues remote from the active sites of enzymes play crucial roles in controlling and shaping the active site for efficient catalysis
Modulating mobility: a paradigm for protein engineering?
- Author
- A Fersht
- A Hnizda
- A Kitao
- AL Pey
- AL Pey
- AS Maltsev
- C Browne
- D Hoffmeister
- D Hoffmeister
- David J. Timson
- DJ Timson
- DJ Timson
- DR Glowacki
- EZ Eisenmesser
- F Huang
- F Zhu
- FJ Kull
- H Kristiansson
- H Wang
- HJ Park
- HJ Park
- HM Berman
- HN Motlagh
- I Waller
- J Chen
- J Ma
- J Otsuka
- J Sun
- J Yang
- J Yang
- J Yang
- JA Brannigan
- JE Ferrell Jr.
- JL Sussman
- JR Schnell
- JR Schnell
- K Teilum
- KA Henzler-Wildman
- KH Roux
- L Skjaerven
- M McAuley
- Margaret McAuley
- MB Quin
- N Doucet
- NC Benson
- NM Goodey
- O Marques
- P Debye
- P Trodler
- R Cole
- RC McDonald
- RM Levy
- SA Wacker
- SC Kamerlin
- WS Bennett Jr.
- WS Bennett Jr.
- WS Bennett Jr.
- Y Shi
- Y Xie
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- 23/07/2016
- Field of study
International Consensus Statement on Rhinology and Allergy: Rhinosinusitis
- Author
- Aanaes K
- Abadie WM
- Abi Najm S
- Abigail P
- Abrahams JJ
- Abrass LJ
- Abreu CB
- Abreu NA
- Abshirini H
- Abuzeid WM
- Abuzeid WM
- Achar P
- Ackerhans M
- Adam P
- Adappa ND
- Adappa ND
- Adappa ND
- Adappa ND
- Adriaensen G
- Agache I
- Aghamohammadi A
- Agius AM
- Agyeman AA
- Ahn CN
- Ahn HJ
- Ahn JC
- Ahn SH
- AhovuoâSaloranta A
- Aitken M
- Ajaiyeoba A
- Akbari E
- Akdis CA
- Akira S
- Akiyama K
- Akiyama K
- Akiyama K
- Al Komser MK
- Alam ES
- Alandejani T
- Alanin MC
- Albritton FDT
- Albu S
- Albu S
- Albu S
- Aldini G
- Alexander NS
- Aljebab F
- Alkire BC
- Allen EK
- Alobid I
- Alobid I
- Alobid I
- Aloulah M
- Alqudah M
- Alromaih S
- Alsaleh S
- Alsharif S
- Alt JA
- Alt JA
- Alt JA
- Alt JA
- Alt JA
- Alves MP
- AlâQudah M
- AlâQudah M.
- AlâQudah M.
- AlâRawi MM
- AlâShaikh S
- AlâShemari H
- AlâSwiahb JN
- Amali A
- Amar YG
- Amble FR
- American Academy of Pediatrics Steering Committee on Quality Improvement and Management (AAP SCQIM)
- Amin MR
- Amine M
- Amodu EJ
- Anamika A
- Anand V
- Anderson DE
- Anderson WC
- Andhale S
- Ankichetty SP
- Annamalai S
- Anon JB
- AnselmoâLima WT
- Antisdel JL
- Antisdel JL
- Antunes MB
- Antunes MB
- Anushiravani M
- Anzai Y
- AnziÄ SA
- Aramani A
- Arden KE
- Arild Danielsen K
- Aring AM
- Arjomandi H
- Armenaka M
- Arnstead N
- Arslan H
- Arslan HH
- Asaka D
- Asero R
- Asero R
- Atighechi S
- Atlas SJ
- Au J
- Aukema AA
- Aurora R
- Autio TJ
- Autio TJ
- Autio TJ
- Autio TJ
- Avdeeva K
- Awad OG
- Awad OGA
- Ayers CM
- Ayoub N
- Ayoub N
- Ayoub N
- Azbell C
- Azila A
- Baba S
- Baba S
- Baba S
- Babela R
- Babinski D
- Bachert C
- Bachert C
- Bachert C
- Bachert C
- Bachert C
- Bachert C
- Bachert C
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- Bachert C
- Bachert C
- Bachert C
- Bachmann G
- Badia L
- Bae JS
- Bagheri SHR
- Baguley C
- Baguley CJ
- Bahtouee M
- Baker TW
- Bakhshaee M
- Balikci HH
- Balikci HH
- Balk EM
- Bang YJ
- Banhiran W
- Banks C
- Banks CA
- Banoub RG
- Baraniuk JN
- Barham HP
- Barham HP
- Barham HP
- Barham HP
- Baroody FM
- Basharat U
- Bassiouni A
- Bassiouni A
- Bassiouni A
- Batikhan H
- Batra PS
- Batra PS
- Batra PS
- Baudoin T
- Baumann A
- Bayonne E
- Becker SS
- Bednarski KA
- Behan L
- Belcher R
- Bendouah Z
- Bengtsson C
- Benjamin MR
- Benninger MS
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- Benninger MS
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- Benoit M
- Bent JP
- Bento LR
- BenĂtez P
- Berg O
- Berger G
- Bergeron M
- BergesâGimeno MP
- Berjis N
- Berlucchi M
- BermudezâBrito M
- Bernstein JA
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- Berry J
- Beswick DM
- Beswick DM
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- Bettadahalli V
- Beule AG
- Beyea JA
- Bezerra T
- Bezerra TF
- Bhalla RK
- Bhalla V
- Bhandarkar ND
- Bhandarkar ND
- Bhandarkar ND
- Bhatt JM
- Bhattacharjee S
- Bhattacharyya N
- Bhattacharyya N
- Bhattacharyya N
- Bhattacharyya N
- Bhattacharyya N
- Bhattacharyya N
- Bhattacharyya N
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- Bhattacharyya N
- Bhattacharyya N
- Bhattacharyya N
- Bhattacharyya N
- Bhattacharyya N
- Bhattacharyya N
- Bhattacharyya N
- Bhattacharyya N
- Bhattacharyya N
- Bhattacharyya N.
- Bhattacharyya N.
- Bhawana G
- Bidder T
- Biedlingmaier JF
- Biedlingmaier JF
- Biedlingmaier JF.
- Biel MA
- Biel MA
- Bikhazi N
- Bikhazi N
- Bilge T
- Biswas K
- Biswas K
- Biswas K
- Bizaki AJ
- Blackwell DL
- Blackwell KE
- Blair C
- Bleier BS
- Bleier BS
- Bleier BS
- Bleier BS
- Blount A
- Boase S
- Boase S
- BockmĂŒhl U
- Boezaart AP
- Bohman A
- Bohman A
- Bohnhorst I
- Boita MM
- Bolger WE
- Bolger WE
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- Bomeli SR
- Bondioni MP
- Bonfils P
- Bonfils P
- Bonfils P
- Bonnomet A
- Boonmak P
- Borish L
- Borsetto D
- Bosse Y
- Bosso JV
- Bothra R
- Bousquet J
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- Brandsted R
- Braun JJ
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- Braunstahl GJ
- Braverman I
- Brescia G
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- Brietzke SE
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- Brodner D
- Brook I
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- BrossâSoriano D
- Brot C
- Brown CL
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- Brozek JL
- Brozek JL
- Brumund KT
- Brunner JP
- Buckley CE
- Buehring I
- Bugten V
- BukowyâBieryllo Z
- Burgstaller JM
- Burton BN
- Bush A
- Businco LD
- Buysschaert ID
- Byun JY
- Cahill KN
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- Calhoun KH
- Calixto NE
- Callejas CA
- Campbell AP
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- Candoni A
- Cannady SB
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- Canonica GW
- Cantrell H.
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- Carlton DA
- Carney AS
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- Carroll WW
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- Chalton R
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- Chandy Z
- Chang CC
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- Chang EH
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- Chang HS
- Chang MT
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- Chang YâS
- Chaudhary N
- Che C
- Chee L
- Chen B
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- Chen CF
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- Chen FH
- Chen H
- Chen JâB
- Chen PH
- Chen X
- Chen YT
- Cheng YK
- Cheon YI
- Chester AC
- Chester AC
- Chester AC
- Chiarella SE
- ChiesaâEstomba CM
- Chin D
- Chinratanapisit S
- Chiu A
- Chiu AG
- Chiu AG
- Chiu AG
- Cho DY
- Cho DY
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- Cho DY
- Cho DY
- Cho GS
- Cho HJ
- Cho JH
- Cho K
- Cho KS
- Cho KS
- Cho SH
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- Chobillon MA
- Choby G
- Choby GW
- Choi EB
- Choi JH
- Chong LY
- Chong LY
- Chong LY
- Chow AW
- Chowdhury NI
- Chowdhury NI
- Christensen DN
- Christensen JM
- Chu DK
- Chung BJ
- Chung SD
- Church CA
- Cirkovic I
- Citardi MJ
- Citardi MJ
- Claeys S
- Claeys S
- Clarhed UKE
- Clark DW
- Clark NM
- Clayman GL
- Cleland EJ
- Cleland EJ
- Cleland EJ
- Clement PA
- Clinger JD
- Clunes LA
- Coates ML
- Codispoti CD
- Coey JG
- Cohen NA
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- Collins FS
- Collins FS
- Collins MM
- Comert S
- Conboy P
- Conger BT
- Conger BT
- Conley DB
- Cope EK
- Copeland E
- Cormier C
- Cormier C
- Cornelius RS
- Cornet ME
- Corradini C
- Corriveau MâN
- Costa Carvalho BT
- Costa ML
- Costa ML
- Costerton JW
- Cottrell J
- Craig JR
- Craig JR.
- Crawley BK
- Criddle MW
- Cronin MJ
- Crosby DL
- Cross JL
- Crotty Alexander LE
- Cryan JF
- Cui XY
- Cui YH
- Cutler J
- Cutler J
- Cutting GR
- Czerny MS
- CÎté DWJ
- D'Anza B
- Dabirmoghaddam P
- Dahlen B
- Dai Q
- Dalgic A
- Dalgorf DM
- Dalm VA
- Daramola OO
- Darveaux J
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- Daudia AT
- Dautremont JF
- Davis GE
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- De Greve G
- De Schryver E
- De Schryver E
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- Dejima K
- Delehaye E
- Delemarre T
- DelGaudio JM
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- DiBaise JK
- DiBaise JK
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- Dietz de Loos DA
- Dijkstra MD
- Dilger AE
- Dilidaer D
- Dilokthornsakul P
- Dingsor G
- Divekar R
- Divekar RD
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- Djupesland PG
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- Doellman MS
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- Dykewicz MS
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- Ebell MH
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- Eberhart LH
- Ebert CS
- Ecevit MC
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- Ediriweera ER
- Eggesbo HB.
- Ehnhage A
- Ehnhage A
- El Mograbi A
- Elborn JS
- Elhakim M
- Eliashar R
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- Eloy JA
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- Eviatar E
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- Expert Panel on Neurologic I
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- Federspil PA
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- Gallant JN
- Galletti B
- Gan EC
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- Gan W
- Gantz O
- Gao WX
- Garbutt JM
- GarciaâRodriguez L
- Garzaro M
- Gehanno P
- Gehanno P
- Gelardi M
- Gelber JT
- Gentile VG
- Georgalas C
- Georgalas C
- Georgalas C
- Geramas I
- Gerber ME
- Gerlinger I
- Gevaert E
- Gevaert P
- Gevaert P
- Gevaert P
- Gevaert P
- Gevaert P
- Gevorgyan A
- Ghegan MD
- Ghegan MD
- Giacchi RJ
- Giacchi RJ
- Gibbons MD
- Giger R
- Gilani S
- Giles WC
- Gillespie MB
- Gion Y
- Giotakis AI
- Giuseppe M
- Glicksman JT
- Gliklich RE
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- Grobler A
- Gross ND
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- Gulati S
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- Gutman M
- Guttenplan MD
- Guven DG
- Gwaltney JJ
- Gwaltney JM
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- Gyawali BR
- GĆobiĆska A
- Ha T
- Ha TN
- Ha TN
- Haberer JP
- Habermann W
- Hadfield P
- Hadfield PJ
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- Hafner B
- Haidar YM
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- Hakansson K
- Halbeisen FS
- Halderman A
- Halderman AA
- Hamner L
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- ZielinskaâBlizniewska H
- Zou L
- Zuckerman JD
- Zurlo JJ
- Zuskin E
- Äulig J
- Publication venue
- 'Wiley'
- Publication date
- 01/01/2021
- Field of study
Background: The 5 years since the publication of the first International Consensus Statement on Allergy and Rhinology: Rhinosinusitis (ICARâRS) has witnessed foundational progress in our understanding and treatment of rhinologic disease. These advances are reflected within the more than 40 new topics covered within the ICARâRSâ2021 as well as updates to the original 140 topics. This executive summary consolidates the evidenceâbased findings of the document. Methods: ICARâRS presents over 180 topics in the forms of evidenceâbased reviews with recommendations (EBRRs), evidenceâbased reviews, and literature reviews. The highest grade structured recommendations of the EBRR sections are summarized in this executive summary. Results: ICARâRSâ2021 covers 22 topics regarding the medical management of RS, which are grade A/B and are presented in the executive summary. Additionally, 4 topics regarding the surgical management of RS are grade A/B and are presented in the executive summary. Finally, a comprehensive evidenceâbased management algorithm is provided. Conclusion: This ICARâRSâ2021 executive summary provides a compilation of the evidenceâbased recommendations for medical and surgical treatment of the most common forms of RS
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- Ăzçelik Ă
- Publication venue
- Elsevier
- Publication date
- 26/02/2023
- Field of study
A preprint version of this article is available at arXiv:2210.00043v2 [hep-ex], https://arxiv.org/abs/2210.00043v2 . Comments: Replaced with the published version. Added the journal reference and the DOI. All the figures and tables, including additional supplementary figures, can be found at https://cms-results.web.cern.ch/cms-results/public-results/publications/B2G-20-009 (CMS Public Pages). Report number: CMS-B2G-20-009, CERN-EP-2022-152.Data availability: see: https://cms-results.web.cern.ch/cms-results/public-results/publications/B2G-20-009 .A search for new heavy resonances decaying to WW, WZ, ZZ, WH, or ZH boson pairs in the all-jets final state is presented. The analysis is based on proton-proton collision data recorded by the CMS detector in 2016-2018 at a centre-of-mass energy of 13 TeV at the CERN LHC, corresponding to an integrated luminosity of 138 fb^{-1}. The search is sensitive to resonances with masses between 1.3 and 6 TeV, decaying to bosons that are highly Lorentz-boosted such that each of the bosons forms a single large-radius jet. Machine learning techniques are employed to identify such jets. No significant excess over the estimated standard model background is observed. A maximum local significance of 3.6 standard deviations, corresponding to a global significance of 2.3 standard deviations, is observed at masses of 2.1 and 2.9 TeV. In a heavy vector triplet model, spin-1 Z' and W' resonances with masses below 4.8 TeV are excluded at the 95% confidence level (CL). These limits are the most stringent to date. In a bulk graviton model, spin-2 gravitons and spin-0 radions with masses below 1.4 and 2.7 TeV, respectively, are excluded at 95% CL. Production of heavy resonances through vector boson fusion is constrained with upper cross section limits at 95% CL as low as 0.1 fb.SCOAP3
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Measurement of the Higgs boson production via vector boson fusion and its decay into bottom quarks in proton-proton collisions at sâ = 13 TeV
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- Publication venue
- Springer Nature on behalf of SISSA
- Publication date
- 30/01/2024
- Field of study
A preprint version of the article is available at arXiv:2308.01253v2 [hep-ex], https://arxiv.org/abs/2308.01253v2 . Comments: Replaced with the published version. Added the journal reference and the DOI. All the figures and tables can be found at https://cms-results.web.cern.ch/cms-results/public-results/publications/HIG-22-009 (CMS Public Pages). Report number: CMS-HIG-22-009, CERN-EP-2023-110.A measurement of the Higgs boson (H) production via vector boson fusion (VBF) and its decay into a bottom quark-antiquark pair (bbÂŻ) is presented using proton-proton collision data recorded by the CMS experiment at sâ = 13 TeV and corresponding to an integrated luminosity of 90.8 fbâ1. Treating the gluon-gluon fusion process as a background and constraining its rate to the value expected in the standard model (SM) within uncertainties, the signal strength of the VBF process, defined as the ratio of the observed signal rate to that predicted by the SM, is measured to be ÎŒqqHHbbÂŻ = 1.01 +0.55â0.46. The VBF signal is observed with a significance of 2.4 standard deviations relative to the background prediction, while the expected significance is 2.7 standard deviations. Considering inclusive Higgs boson production and decay into bottom quarks, the signal strength is measured to be ÎŒincl.HbbÂŻ = 0.99 +0.48â0.41, corresponding to an observed (expected) significance of 2.6 (2.9) standard deviations.SCOAP3, STFC; Marie-Curie program and the European Research Council and Horizon 2020 Gran
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