Syma Khalid @ProfSyK Twitter profile | Pikagi

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Syma Khalid

@ProfSyK

8,222

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2,731

Following

1,269

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25,822

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Prof of Computational Microbiology. Oxford Biochemistry & St Anne’s College. Bacterial Cell Envelopes. Chair of @hecbiosim . #computationalmicrobiology #LFC 🌈

Oxford, England

https://t.co/hrDO3PUBSI

Joined July 2011

Don't wanna be here? Send us removal request.

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@ProfSyK

Syma Khalid

2 years

We are looking to hire a PDRA next year, likely February/March time. Anyone interested in working with us @SKhalidLab on multiscale simulation method dev please contact me mid January-ish I will not be checking emails over the holiday period, but very happy to chat after that!

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@ProfSyK

Syma Khalid

5 years

@Simcoe_Kid @AdamCatterall Well done Gary! Has the courage of his convictions. Standing with you (and I’m a Liverpool fan).

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@ProfSyK

Syma Khalid

3 years

So, some big personal & professional news folks. I will be moving to Oxford in August of this year as Assoc Prof in Molecular and Cellular Biochemistry and Tutorial Fellow at St Anne’s. This comes after 14 happy years at Southampton.

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@ProfSyK

Syma Khalid

3 years

Thrilled to have officially been awarded the title of ‘Professor of Computational Microbiology’ for the start in Oxford. 😀

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@ProfSyK

Syma Khalid

2 years

Wish folk would stop expecting to learn MD ‘quickly’ to finish off a project or to generate data where experiments have failed. It doesn’t work like that. Seriously.

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@ProfSyK

Syma Khalid

2 years

Simulation support for projects is not free, folks. Please do cost your simulation partners into grant proposals wherever you can. Simulations need lots of training & usually need project dedicated researchers, especially where parameterisation or non-standard methods are needed

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@ProfSyK

Syma Khalid

1 year

Me and GFP. A match made in heaven one could say?

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@ProfSyK

Syma Khalid

3 years

Just got the award letter for EPSRC Established Career fellowship. We’ll be using simulations in combination with new imaging methods to study bacterial cell envelopes. In part collaboration with @basham_mark at @RosFrankInst . The fellowship will get the Oxf team up and running.

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@ProfSyK

Syma Khalid

3 years

Love Oxford, left 14 years ago, returned today & got my old username back :) 😍

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@ProfSyK

Syma Khalid

3 years

Joachim Löw always looks like his best paper has been desk rejected from Scientific Reports.

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@ProfSyK

Syma Khalid

3 years

New work digs. Not too shabby.

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@ProfSyK

Syma Khalid

3 years

I’m properly English. I was born in Wolverhampton, for goodness sake. Yet somehow in the eyes of some I’m less English than those with paler skin. When such sentiments emerge they don’t cut as deeply as previously, but they do nag away, never quite allowing one to fully relax.

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@ProfSyK

Syma Khalid

9 months

Postdoc position available in my lab in Oxford. Running massive bacterial simulations on HPC resources & augmenting the sims with AI methods for greater efficiency. Funded via @hecbiosim & in collaboration with @arvindr_ at Argonne National Lab. pls RT

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@ProfSyK

Syma Khalid

3 years

I don’t get the ‘we should help India because otherwise it will impact on us too’. How about we help India because they are in need & it is the right thing to do?

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@ProfSyK

Syma Khalid

3 years

Whoop we have made the cover of @Structure_CP . An image from @ConradoPedebos paper in which he describes our crowded model of the E. coli periplasm. Image made using @proteinimaging

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@ProfSyK

Syma Khalid

3 years

The longest MD simulation in my PhD thesis was 10 ns (~50k atoms). I have just performed an energy minimisation (5000 steps) on a (coarse-grained) system of over 1m atoms on my laptop. Feck, I’m old.

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@ProfSyK

Syma Khalid

2 years

The best #bps2022 badge I’ve had to date :)

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@ProfSyK

Syma Khalid

1 year

Some really nice news yesterday: I’ll be a 2023-2024 Flatiron Institute IDEA Scholar. Looking forward to spending some time in New York City! @FlatironCCB @FlatironInst @SimonsFdn

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@ProfSyK

Syma Khalid

3 years

A few more dramas today, but we are now moving our stuff in! Hurrah.

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@ProfSyK

Syma Khalid

2 years

Lots of academia bashing on here recently. It’s not perfect at all - loads of jobs aren’t. But lots of us love what we do - I hope that doesn’t get lost in all the bashing.

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@ProfSyK

Syma Khalid

5 years

@agrossfield @LindaColumbus Im always tempted to say something completely untruthful but exotic sounding ‘oh I train baby giraffes how to walk with good posture, for a living’

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@ProfSyK

Syma Khalid

4 years

I’m 42. Mum is stressing about my hair & clothing for sister’s wedding in August (all in line with govt guidelines). To calm her, I’ve told her I will match my hair colour to my suit. This seems to have made things worse. #cantwin

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@ProfSyK

Syma Khalid

4 years

We wrote a Methods article to provide a practical guide to setting up MD simulations of membrane proteins: #compchem #biophysics

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@ProfSyK

Syma Khalid

9 months

Preparing a lecture - time is limited, so I spent 2 hours making a graphic showing an antibiotic tablet wielding a sword and shield as it attacks a bacterium. It seemed like a good use of time, but upon reflection…

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@ProfSyK

Syma Khalid

3 years

Goodness me how gracious are both of these tennis players. The kids are alright!

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@ProfSyK

Syma Khalid

4 years

Parting the E.coli outer membrane - I am the Moses of bacterial membranes... (at least this time I parted it deliberately and didn’t just leave waters in the wrong place in the simulations)

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@ProfSyK

Syma Khalid

4 years

Delighted to have made the cover of @Structure_CP with @storzlab @AndrzejSzH - my former postdoc Firdaus Samsudin (now at A*STAR, Singapore) put the image together in photoshop.

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@ProfSyK

Syma Khalid

4 months

My badge is growing longer! #BPS2024 @BiophysicalSoc

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@ProfSyK

Syma Khalid

2 years

What a year. Family health scares (ongoing), dream job secured, dream fellowship secured, stressful house move, break-in following the stressful house move, constant shadow of covid, but still standing & still smiling. Happy new year, friends- may 2022 bring much happiness.

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@ProfSyK

Syma Khalid

2 years

New group logo: @SKhalidLab

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@ProfSyK

Syma Khalid

2 years

Pretty chuffed with this pic I got this evening. Bangkok Tuktuk

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@ProfSyK

Syma Khalid

4 years

There are going to be a lot of modelling & simulation studies on sars-cov2 components that won’t get published due to being scooped, shown to be irrelevant or simply wrong. So folks, please look after the interests of your PhD students & postdocs. Design the studies responsibly.

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@ProfSyK

Syma Khalid

3 years

Come work with us in Oxford Biochemistry. We have an opening for a PDRA position to work on coarse-grained models of various macromolecules. Please RT

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@ProfSyK

Syma Khalid

2 years

When rushing to get to Heathrow to be external examiner, DO NOT stop at the world food market to purchase spicy fish curry. DO NOT put said curry into the bag containing your clothes. DO NOT then run for the bus to the airport. DO NOT tip bag. Who would do that??

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@ProfSyK

Syma Khalid

4 years

Colleagues & friends with kids - we have updated the colouring in pages on our website: Please feel free to print out and give to kids to colour in. Send us completed copies and we will upload a few to the website with name and school of kid.

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@ProfSyK

Syma Khalid

2 years

Which tweeps are going to San Fran for BPS? I’m ridiculously excited about the meeting this year @BiophysicalSoc

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@ProfSyK

Syma Khalid

3 years

Artwork ready for the walls. I am doing real work today too…promise

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@ProfSyK

Syma Khalid

5 years

@cushdela @Simcoe_Kid @AdamCatterall It demonstrates that I stand with Gary through and through and that this is bigger than any footballing rivalry. That is all. Have a great Christmas and New Year.

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@ProfSyK

Syma Khalid

3 years

Bit tired of hearing ‘be good to people while you are on the way up, because you will meet them again when you are on the way down’. How about ‘be good to people without any other motivation than it’s the right thing to do’?

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@ProfSyK

Syma Khalid

2 years

I love football. But I’ve decided I cannot justify watching the World Cup in Qatar. Stadiums built by slaves. Gays persecuted. Laws that are hostile to non-Muslims. This cannot be right. It will be tough as friends and family will watch. But at some point something has to matter

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@ProfSyK

Syma Khalid

3 years

Last day of being employed by @UoSChemistry . Lots of memories eg: the pigeon that pooped on the exam papers the first time I was asked to start an exam. Another: falling into the pond while reading my email on phone en route to give a lecture. But mostly: my awesome colleagues.

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@ProfSyK

Syma Khalid

2 years

@AnfieldWatch Jesus. Would be good to see Muhammed and Jesus lead attack for us 😂

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@ProfSyK

Syma Khalid

3 years

11-month postdoc position in my lab at Oxford due to be advertised soon. Immediate start. Please keep a look out on my group website.

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@ProfSyK

Syma Khalid

3 years

Cell envelope rendering this evening to celebrate acceptance of @ConradoPedebos paper. Details soon! A nice way to start 2021

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@ProfSyK

Syma Khalid

4 years

Recorded the last lecture of the term dressed as Santa. He beard was bit cumbersome. Hope the students don’t think it’s weird.

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@ProfSyK

Syma Khalid

3 years

Dad taking a pic of mum outside our house. Love this pic

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@ProfSyK

Syma Khalid

2 years

Our paper on Uncovering cryptic pockets in the SARS-CoV-2 spike glycoprotein using benzene probes in MD simulations validated by HDX MS is out. Big collaborative effort led by Peter Bond (A*STAR) with @GaneshSAnand1

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@ProfSyK

Syma Khalid

4 years

Slightly irritated by the number of folk knocking academia - it is not perfect of course (what is?) but in the grand scheme of things it’s wonderful. Mostly we work on topics that interest us and we have much freedom. Would be good to see some ❤️ for this vocation.

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@ProfSyK

Syma Khalid

2 years

The mdp file must never be a stranger. Be able to explain & justify every single line #gromacs #gmx

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@ProfSyK

Syma Khalid

15 days

Position available in my group. Another one coming up! Come join us at Oxford Postdoctoral research associate in Large-scale simulations of the E. coli cell envelope at University of Oxford

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Postdoctoral research associate in Large-scale simulations of the E. coli cell envelope at Univer...

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@ProfSyK

Syma Khalid

5 months

Dear wet lab PIs - do not guilt trip comp folk to agree to be collaborators in grants proposals without costing people in for us. There are no magic MD elves - someone has to do the simulations! 🙏🏽 #compchem

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@ProfSyK

Syma Khalid

2 years

Come join us! Two post doc positions available in my lab at Oxford, funded by EPSRC. We are seeking to develop new computational models of bacterial cell envelopes in collaboration with @RosFrankInst & @basham_mark please see: #biophysics #compchem pls RT

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@ProfSyK

Syma Khalid

2 years

Walking over to Merton for dinner. It’s rather a picturesque evening. Now if only my photography could do it justice….

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@ProfSyK

Syma Khalid

3 years

Looks like we’ll be hiring a postdoc to join the group in Oxford in the very near future. Exciting project, details coming soon!

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@ProfSyK

Syma Khalid

5 years

Flight attendant: Is there a doctor on this flight? Dad: *nudging me* that should've been you Me: Not now Dad Dad: Not asking for a comp. biophysicist to help, are they? Me: Dad, there's a medical emergency happening right now Dad: Go and see if ‘enhanced sampling’ helps

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@ProfSyK

Syma Khalid

3 years

My first in-person talk in hundreds of years…

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@ProfSyK

Syma Khalid

2 years

Our latest collaboration with (and led by) Bert van den Berg: Structural basis for host recognition and superinfection exclusion by bacteriophage T5. Structural biology, simulations and experimental microbiology Sims by @AstridBrandner and Sophie Mader

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Structural basis for host recognition and superinfection exclusion by bacteriophage T5 | PNAS

A key but poorly understood stage of the bacteriophage life cycle is the binding of phage receptor-binding proteins (RBPs) to receptors on the host...

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@ProfSyK

Syma Khalid

3 years

England fans: it would be great to send messages of support to Sancho, Rashford and particularly Saka. Three players of colour who missed penalties - the Neanderthals will no doubt send abuse their way. So please let’s also send support.

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@ProfSyK

Syma Khalid

2 years

My hairy pink new shoes arrived. Rather pleased with them. The other half is less than impressed. Ah well.

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@ProfSyK

Syma Khalid

4 years

Thanks for this @BiophysicalSoc - & for allowing me to get Jurgen Klopp into the article too :) #biophysics #LFC

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@ProfSyK

Syma Khalid

3 years

Oxford is certainly photogenic this evening.

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@ProfSyK

Syma Khalid

2 years

What does it mean to ‘look’ British?

@robertbrynin

R S Brynin, Anglo-Jewish Author

2 years

@petemorristwit Regardless of one's concern about appearing racist, I think we have to accept that a large number of Britons are uneasy about being governed by politicians who don't 'look' British, and whose names they can't pronounce.

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@ProfSyK

Syma Khalid

2 years

Ah #bps2022 feels like coming home tbh. Just heard a great talk by @ScheuringLab at the Membrane Structure & Function subgroup. Question from Lukas Tamm. All familiar faces & names speaking & in the audience - so good to be back! @BiophysicalSoc

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@ProfSyK

Syma Khalid

2 years

Folk very often mispronounce my name as Seema. I dunno why after all these years I still don’t correct it first time it happens- then it goes past the point of correcting. So I’ll just tweet it- it’s pronounced like ‘Sigh-ma’. Thanks 😀👍🏽

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@ProfSyK

Syma Khalid

9 months

We are resuming the @MicrobioSoc supported online seminar series on bacterial cell envelopes soon. Please do let us know if you would like to speak or nominate someone else. These are supportive, inclusive, seminars free to anyone interested in bacterial cell envelopes. Pls RT

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@ProfSyK

Syma Khalid

2 years

Membrane Structure & Function subgroup dinner was a lot of fun this evening. @birloque @BarreraLab @VeatchLab @ZenoResearch @LeventalLab and many others! @BiophysicalSoc #bps2022

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@ProfSyK

Syma Khalid

2 years

Moved into new office in phase2 of the New Biochemistry building. Pretty happy with it. I suspect once @philbiggin moves next door I’ll start complaining 😉😉

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@ProfSyK

Syma Khalid

4 years

There was a Twitter trend recently about one’s favourite self photograph. I missed that. But here’s mine; my mum, dad and I in Murree, Pakistan, when I was ~3 years old.

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@ProfSyK

Syma Khalid

3 years

Biochemistry at St Anne’s new era kicks off. @StAnnesCollege 🙌🏾💪🏾

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@ProfSyK

Syma Khalid

2 years

Totally bonkers occurrence today. We appear to have become a stop on a tourist trail. A coach pulled up outside the house, bunch of tourists came up the drive and took pics of the house & selfies. World has gone bonkers

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@ProfSyK

Syma Khalid

2 years

Went out for a walk to do some street photography in San Fran. This pic I think sums up the US ideal for me, the Stars & Stripes, the rainbow flag with the New Delhi Indian restaurant in the background. In other words national pride AND celebration of diversity. #bps2022

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@ProfSyK

Syma Khalid

2 years

Loving the @MicrobioSoc #Microbio22 Microbiology Society conference in Belfast. It’s my first time at this meeting & I’m wondering why it’s taken me so long to discover it. Bugs and more bugs everywhere. Marvellous!

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@ProfSyK

Syma Khalid

2 years

The global MD simulation community is pretty cool. So much support, like emailing two very busy colleagues in other institutions about comments on a short article I’m writing, and receiving them within minutes! Mind blown. Thank you amigas

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@ProfSyK

Syma Khalid

5 years

Inspired by @dsgoodsell - rendering images from our latest sims. Here’s the E. coli outer membrane, a bunch of periplasmic proteins, the cell wall and a mystery antibiotic

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@ProfSyK

Syma Khalid

4 months

It’s out! Iain’s @ipssmith first 1st author paper - we show that the local molecular environment can alter the binding modes of macromolecules within the E. coli periplasm. In this case polymyxins with local proteins and the cell wall.

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Molecular Crowding Alters the Interactions of Polymyxin Lipopeptides within the Periplasm of E....

The cell envelope of Gram-negative bacteria is a crowded tripartite architecture that separates the cell interior from the external environment. Two membranes encapsulate the aqueous periplasm, which...

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@ProfSyK

Syma Khalid

2 years

San Fran. Nice to see you again, old friend

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@ProfSyK

Syma Khalid

3 years

Festive vibes in the department - early start to get ready for admissions today.

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@ProfSyK

Syma Khalid

5 years

Just been talking to my dad. He’s just finished his job after 44 years as a bus driver. So proud of him. He introduced me to LFC too. He took a few mins to talk about the game before going off to his leaving do. God bless awesome parents 😍

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@ProfSyK

Syma Khalid

9 months

Oxford 😍😍

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@ProfSyK

Syma Khalid

9 months

Come work in my lab in Oxford Biochemistry- Postdoc funded via @hecbiosim in collab with @arvindr_ at Argonne National Lab. We will do massive bacterial membrane simulations augmented with ML. . We are friendly, supportive lab in a beautiful city.

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@ProfSyK

Syma Khalid

4 months

Congratulations @RommieAmaro and @LindorffLarsen on being elected as Biophysical Society Fellows. Flying the flag for not only computational studies but also for integrity, excellent mentorship and community building 🙌🏾👌🏾

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@ProfSyK

Syma Khalid

3 years

Been Oxford-AZ ed 💪🏾

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@ProfSyK

Syma Khalid

2 years

Had a lot of fun writing this. @RommieAmaro @ElisaTelisa @HummerLab are featured!

@NatureRevMicro

Nature Reviews Microbiology

@NatureRevMicro

2 years

Simulations of the spike: molecular dynamics and SARS-CoV-2 This Under the Lens discusses a few of the growing number of molecular simulation studies that have made contributions towards our mechanistic understanding of the spike protein of SARS-CoV-2

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@ProfSyK

Syma Khalid

3 years

Pride month socks/shoe combo ready for my talk at the @CompChemURG event today on inclusivity and equality in Computational Chemistry. Thank you to @MgmsUpdates and @RoySocChem for funding this excellent event.

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@ProfSyK

Syma Khalid

4 years

Some cathartic image making this evening, after a long shift at the office.

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@ProfSyK

Syma Khalid

1 year

It’s out! @KahlanNewman ’s second paper of 2023. A prediction of substrate (an antibiotic & a bile acid) extrusion from the outer membrane component of an efflux pump from C. jejuni. Weirdly the protein is N-glycosylated. . #glycotime

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Conformational dynamics and putative substrate extrusion pathways of the N-glycosylated outer...

Author summary Campylobacter jejuni is a Gram-negative bacterium that is a major cause of gastroenteritis. Infection is also associated with the development of some auto-immune conditions. Therefore,...

journals.plos.org

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@ProfSyK

Syma Khalid

2 years

A few more days to apply for a postdoc position in my group at Oxford. Come join us to help develop coarse-grain models of macromolecules

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@ProfSyK

Syma Khalid

4 years

Announcing the 1st of our bacterial cell envelopes meetings. Great speakers lined up. We are planning more virtual meetings to bring the molecular bacterial cell envelope community together. Details soon at: @RadfordLab @TBharat_lab @Figlegend @CharmmGui

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@ProfSyK

Syma Khalid

4 years

Merry Christmas & a restful festive season from the bacterial cell envelope obsessed of Southampton :)

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@ProfSyK

Syma Khalid

3 years

First term at Oxford done - that was intense, tiring, but mostly loads of fun 🙌🏾

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@ProfSyK

Syma Khalid

1 year

New group photo 😍

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@ProfSyK

Syma Khalid

10 months

Like many others, my mentors have played a role in shaping me that is immeasurable. I was fortunate to host three of them at my place this evening @CVR_Research @carolr24 @Armitage_Judy and Alison Rodger. The debt I owe to all three is huge. Thank you & here’s to future fun 🙏🏽

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@ProfSyK

Syma Khalid

5 months

Tutorial today. Me: nature doesn’t like vacuums. Student: yeah, my dog hates the hoover. Tweeted with permission of student.

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@ProfSyK

Syma Khalid

4 years

We really must stop having 1 hour back to back virtual meetings. Else the days become extremely difficult- furthermore it cannot be good for the eyes, back etc, surely?It is relentless at the moment. We are working more intensely now than in non-covid times in academia, I think?

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@ProfSyK

Syma Khalid

4 months

We launched our @wellcometrust Discovery award on ‘Redefining the Gram Negative Bacterial Outer Membrane’ today. A diverse team led by Colin Kleanthous featuring Lindsay Baker Shabaz Mohammed @hoogenboom_lab , Ben Davis, @MelissaWebby & @joszczepaniak @KleanthousLab @SKhalidLab

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@ProfSyK

Syma Khalid

2 years

Last week of my 1st academic year at Oxford. Been a case of flying by the seat of my pants while negotiating the Oxford tutorial system, looking after research team in 2 diff universities & catching up with postponed conferences. It’s been great fun! @OxBiochNews @StAnnesCollege

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@ProfSyK

Syma Khalid

2 years

The new workstation is pretty snazzy. Now if it only it could run the calculations by itself…

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@ProfSyK

Syma Khalid

2 years

There are a lot of folk on Twitter telling academics how to run our research groups. Hope they all have spotless track records of supervision, publication, grant income etc. If not, please do have some respect for the experiences of others and refrain from absolute statements 🙏🏽

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@ProfSyK

Syma Khalid

2 years

Went for a pseudo-goth grumpy Professor vibe.

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@ProfSyK

Syma Khalid

3 years

Behold: the great Sakura tree of Winchester.

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@ProfSyK

Syma Khalid

9 months

The funding & publishing gods have smiled on @SKhalidLab this week. While its wonderful to celebrate the good times, it’s also important to remember the times in the wilderness & remember that not being funded is not necessarily indicative of scientific quality. #solidarity

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